[English] 日本語
Yorodumi
- PDB-6dwu: Crystal structure of complex of BBKI and Bovine Trypsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dwu
TitleCrystal structure of complex of BBKI and Bovine Trypsin
Components
  • Cationic trypsin
  • Kunitz-type inihibitor
KeywordsHYDROLASE / BBKI
Function / homology
Function and homology information


endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. ...Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease 1 / Kunitz-type inihibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Bauhinia bauhinioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.96 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes.
Authors: Li, M. / Srp, J. / Gustchina, A. / Dauter, Z. / Mares, M. / Wlodawer, A.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Cationic trypsin
AB: Kunitz-type inihibitor
AC: Cationic trypsin
AD: Kunitz-type inihibitor
AE: Cationic trypsin
AF: Kunitz-type inihibitor
AG: Cationic trypsin
AH: Kunitz-type inihibitor
AI: Cationic trypsin
AJ: Kunitz-type inihibitor
AK: Cationic trypsin
AL: Kunitz-type inihibitor
AM: Cationic trypsin
AN: Kunitz-type inihibitor
AO: Cationic trypsin
AP: Kunitz-type inihibitor
AQ: Cationic trypsin
AR: Kunitz-type inihibitor
AS: Cationic trypsin
AT: Kunitz-type inihibitor
AU: Cationic trypsin
AV: Kunitz-type inihibitor
BA: Cationic trypsin
BB: Kunitz-type inihibitor
BC: Cationic trypsin
BD: Kunitz-type inihibitor
BE: Cationic trypsin
BF: Kunitz-type inihibitor
BG: Cationic trypsin
BH: Kunitz-type inihibitor
BI: Cationic trypsin
BJ: Kunitz-type inihibitor
BK: Cationic trypsin
BL: Kunitz-type inihibitor
BM: Cationic trypsin
BN: Kunitz-type inihibitor
BO: Cationic trypsin
BP: Kunitz-type inihibitor
BQ: Cationic trypsin
BR: Kunitz-type inihibitor
BS: Cationic trypsin
BT: Kunitz-type inihibitor
BU: Cationic trypsin
BV: Kunitz-type inihibitor
CA: Cationic trypsin
CB: Kunitz-type inihibitor
CC: Cationic trypsin
CD: Kunitz-type inihibitor
CE: Cationic trypsin
CF: Kunitz-type inihibitor
CG: Cationic trypsin
CH: Kunitz-type inihibitor
CI: Cationic trypsin
CJ: Kunitz-type inihibitor
CK: Cationic trypsin
CL: Kunitz-type inihibitor
CM: Cationic trypsin
CN: Kunitz-type inihibitor
CO: Cationic trypsin
CP: Kunitz-type inihibitor
CQ: Cationic trypsin
CR: Kunitz-type inihibitor
CS: Cationic trypsin
CT: Kunitz-type inihibitor
CU: Cationic trypsin
CV: Kunitz-type inihibitor
DA: Cationic trypsin
DB: Kunitz-type inihibitor
DC: Cationic trypsin
DD: Kunitz-type inihibitor
DE: Cationic trypsin
DF: Kunitz-type inihibitor
DG: Cationic trypsin
DH: Kunitz-type inihibitor
DI: Cationic trypsin
DJ: Kunitz-type inihibitor
DK: Cationic trypsin
DL: Kunitz-type inihibitor
DM: Cationic trypsin
DN: Kunitz-type inihibitor
DO: Cationic trypsin
DP: Kunitz-type inihibitor
DQ: Cationic trypsin
DR: Kunitz-type inihibitor
DS: Cationic trypsin
DT: Kunitz-type inihibitor
DU: Cationic trypsin
DV: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)1,811,19688
Polymers1,811,19688
Non-polymers00
Water0
1
AA: Cationic trypsin
AB: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-9 kcal/mol
Surface area15350 Å2
MethodPISA
2
AC: Cationic trypsin
AD: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-8 kcal/mol
Surface area15450 Å2
MethodPISA
3
AE: Cationic trypsin
AF: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-7 kcal/mol
Surface area15300 Å2
MethodPISA
4
AG: Cationic trypsin
AH: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-8 kcal/mol
Surface area15350 Å2
MethodPISA
5
AI: Cationic trypsin
AJ: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area15230 Å2
MethodPISA
6
AK: Cationic trypsin
AL: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area15450 Å2
MethodPISA
7
AM: Cationic trypsin
AN: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-9 kcal/mol
Surface area15250 Å2
MethodPISA
8
AO: Cationic trypsin
AP: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-6 kcal/mol
Surface area15390 Å2
MethodPISA
9
AQ: Cationic trypsin
AR: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-8 kcal/mol
Surface area15390 Å2
MethodPISA
10
AS: Cationic trypsin
AT: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area15350 Å2
MethodPISA
11
AU: Cationic trypsin
AV: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9 kcal/mol
Surface area15320 Å2
MethodPISA
12
BA: Cationic trypsin
BB: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-9 kcal/mol
Surface area15350 Å2
MethodPISA
13
BC: Cationic trypsin
BD: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-5 kcal/mol
Surface area15460 Å2
MethodPISA
14
BE: Cationic trypsin
BF: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area15430 Å2
MethodPISA
15
BG: Cationic trypsin
BH: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area15400 Å2
MethodPISA
16
BI: Cationic trypsin
BJ: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-6 kcal/mol
Surface area15340 Å2
MethodPISA
17
BK: Cationic trypsin
BL: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-8 kcal/mol
Surface area15390 Å2
MethodPISA
18
BM: Cationic trypsin
BN: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-7 kcal/mol
Surface area15420 Å2
MethodPISA
19
BO: Cationic trypsin
BP: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-9 kcal/mol
Surface area15420 Å2
MethodPISA
20
BQ: Cationic trypsin
BR: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-6 kcal/mol
Surface area15300 Å2
MethodPISA
21
BS: Cationic trypsin
BT: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-6 kcal/mol
Surface area15310 Å2
MethodPISA
22
BU: Cationic trypsin
BV: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-9 kcal/mol
Surface area15410 Å2
MethodPISA
23
CA: Cationic trypsin
CB: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-9 kcal/mol
Surface area15360 Å2
MethodPISA
24
CC: Cationic trypsin
CD: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-6 kcal/mol
Surface area15370 Å2
MethodPISA
25
CE: Cationic trypsin
CF: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area15310 Å2
MethodPISA
26
CG: Cationic trypsin
CH: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-8 kcal/mol
Surface area15300 Å2
MethodPISA
27
CI: Cationic trypsin
CJ: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-8 kcal/mol
Surface area15420 Å2
MethodPISA
28
CK: Cationic trypsin
CL: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-6 kcal/mol
Surface area15250 Å2
MethodPISA
29
CM: Cationic trypsin
CN: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area15290 Å2
MethodPISA
30
CO: Cationic trypsin
CP: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-7 kcal/mol
Surface area15460 Å2
MethodPISA
31
CQ: Cationic trypsin
CR: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area15250 Å2
MethodPISA
32
CS: Cationic trypsin
CT: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area15230 Å2
MethodPISA
33
CU: Cationic trypsin
CV: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-7 kcal/mol
Surface area15610 Å2
MethodPISA
34
DA: Cationic trypsin
DB: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-7 kcal/mol
Surface area15460 Å2
MethodPISA
35
DC: Cationic trypsin
DD: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area15240 Å2
MethodPISA
36
DE: Cationic trypsin
DF: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-8 kcal/mol
Surface area15310 Å2
MethodPISA
37
DG: Cationic trypsin
DH: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area15410 Å2
MethodPISA
38
DI: Cationic trypsin
DJ: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-7 kcal/mol
Surface area15460 Å2
MethodPISA
39
DK: Cationic trypsin
DL: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-10 kcal/mol
Surface area15300 Å2
MethodPISA
40
DM: Cationic trypsin
DN: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9 kcal/mol
Surface area15400 Å2
MethodPISA
41
DO: Cationic trypsin
DP: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-7 kcal/mol
Surface area15320 Å2
MethodPISA
42
DQ: Cationic trypsin
DR: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-7 kcal/mol
Surface area15360 Å2
MethodPISA
43
DS: Cationic trypsin
DT: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-11 kcal/mol
Surface area15270 Å2
MethodPISA
44
DU: Cationic trypsin
DV: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)41,1642
Polymers41,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.167, 483.880, 137.010
Angle α, β, γ (deg.)90.000, 116.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain AB
21chain AD
31chain AF
41chain AH
51chain AJ
61chain AL
71chain AN
81chain AP
91chain AR
101chain AT
111chain AV
121chain BB
131chain BD
141chain BF
151chain BH
161chain BJ
171chain BL
181chain BN
191chain BP
201chain BR
211chain BT
221chain BV
231chain CB
241chain CD
251chain CF
261chain CH
271chain CJ
281chain CL
291chain CN
301chain CP
311chain CR
321chain CT
331chain CV
341chain DB
351chain DD
361chain DF
371chain DH
381chain DJ
391chain DL
401chain DN
411chain DP
421chain DR
431chain DT
441chain DV
12chain AA
22chain AC
32chain AE
42chain AG
52chain AI
62chain AK
72chain AM
82chain AO
92chain AQ
102chain AS
112chain AU
122chain BA
132chain BC
142chain BE
152chain BG
162chain BI
172chain BK
182chain BM
192chain BO
202chain BQ
212chain BS
222chain BU
232chain CA
242chain CC
252chain CE
262chain CG
272chain CI
282chain CK
292chain CM
302chain CO
312chain CQ
322chain CS
332chain CU
342chain DA
352chain DC
362chain DE
372chain DG
382chain DI
392chain DK
402chain DM
412chain DO
422chain DQ
432chain DS
442chain DU

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain ABAB1 - 163
211chain ADAD1 - 163
311chain AFAF1 - 163
411chain AHAH1 - 163
511chain AJAJ1 - 163
611chain ALAL1 - 163
711chain ANAN1 - 163
811chain APAP1 - 163
911chain ARAR1 - 163
1011chain ATAT1 - 163
1111chain AVAV1 - 163
1211chain BBBB1 - 163
1311chain BDBD1 - 163
1411chain BFBF1 - 163
1511chain BHBH1 - 163
1611chain BJBJ1 - 163
1711chain BLBL1 - 163
1811chain BNBN1 - 163
1911chain BPBP1 - 163
2011chain BRBR1 - 163
2111chain BTBT1 - 163
2211chain BVBV1 - 163
2311chain CBCB1 - 163
2411chain CDCD1 - 163
2511chain CFCF1 - 163
2611chain CHCH1 - 163
2711chain CJCJ1 - 163
2811chain CLCL1 - 163
2911chain CNCN1 - 163
3011chain CPCP1 - 163
3111chain CRCR1 - 163
3211chain CTCT1 - 163
3311chain CVCV1 - 163
3411chain DBDB1 - 163
3511chain DDDD1 - 163
3611chain DFDF1 - 163
3711chain DHDH1 - 163
3811chain DJDJ1 - 163
3911chain DLDL1 - 163
4011chain DNDN1 - 163
4111chain DPDP1 - 163
4211chain DRDR1 - 163
4311chain DTDT1 - 163
4411chain DVDV1 - 163
112chain AAAA16 - 238
212chain ACAC16 - 238
312chain AEAE16 - 238
412chain AGAG16 - 238
512chain AIAI16 - 238
612chain AKAK16 - 238
712chain AMAM16 - 238
812chain AOAO16 - 238
912chain AQAQ16 - 238
1012chain ASAS16 - 238
1112chain AUAU16 - 238
1212chain BABA16 - 238
1312chain BCBC16 - 238
1412chain BEBE16 - 238
1512chain BGBG16 - 238
1612chain BIBI16 - 238
1712chain BKBK16 - 238
1812chain BMBM16 - 238
1912chain BOBO16 - 238
2012chain BQBQ16 - 238
2112chain BSBS16 - 238
2212chain BUBU16 - 238
2312chain CACA16 - 238
2412chain CCCC16 - 238
2512chain CECE16 - 238
2612chain CGCG16 - 238
2712chain CICI16 - 238
2812chain CKCK16 - 238
2912chain CMCM16 - 238
3012chain COCO16 - 238
3112chain CQCQ16 - 238
3212chain CSCS16 - 238
3312chain CUCU16 - 238
3412chain DADA16 - 238
3512chain DCDC16 - 238
3612chain DEDE16 - 238
3712chain DGDG16 - 238
3812chain DIDI16 - 238
3912chain DKDK16 - 238
4012chain DMDM16 - 238
4112chain DODO16 - 238
4212chain DQDQ16 - 238
4312chain DSDS16 - 238
4412chain DUDU16 - 238

NCS ensembles :
ID
1
2

-
Components

#1: Protein ...
Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein ...
Kunitz-type inihibitor


Mass: 17839.266 Da / Num. of mol.: 44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Description: The authors state that this structure was determined at low resolution and its primary aim was to determine the arrangement of the molecules in the unit cell, rather than provide ...Description: The authors state that this structure was determined at low resolution and its primary aim was to determine the arrangement of the molecules in the unit cell, rather than provide detailed information about the protein complexes. The latter information is available for crystals grown in a different space group.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 17.5% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.96→50 Å / Num. obs: 124813 / % possible obs: 88.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rpim(I) all: 0.07 / Rrim(I) all: 0.153 / Rsym value: 0.135 / Net I/σ(I): 8.16
Reflection shellResolution: 3.96→4.03 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.01 / Num. unique obs: 2619 / Rpim(I) all: 0.201 / Rrim(I) all: 0.346 / Rsym value: 0.279 / % possible all: 37.3

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.96→49.23 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.91
RfactorNum. reflection% reflection
Rfree0.2815 5830 4.92 %
Rwork0.226 --
obs0.2288 118576 85.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.81 Å2 / Biso mean: 71.2828 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 3.96→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms127116 0 0 0 127116
Num. residues----16984
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11AB34968X-RAY DIFFRACTION5.494TORSIONAL
12AD34968X-RAY DIFFRACTION5.494TORSIONAL
13AF34968X-RAY DIFFRACTION5.494TORSIONAL
14AH34968X-RAY DIFFRACTION5.494TORSIONAL
15AJ34968X-RAY DIFFRACTION5.494TORSIONAL
16AL34968X-RAY DIFFRACTION5.494TORSIONAL
17AN34968X-RAY DIFFRACTION5.494TORSIONAL
18AP34968X-RAY DIFFRACTION5.494TORSIONAL
19AR34968X-RAY DIFFRACTION5.494TORSIONAL
110AT34968X-RAY DIFFRACTION5.494TORSIONAL
111AV34968X-RAY DIFFRACTION5.494TORSIONAL
112BB34968X-RAY DIFFRACTION5.494TORSIONAL
113BD34968X-RAY DIFFRACTION5.494TORSIONAL
114BF34968X-RAY DIFFRACTION5.494TORSIONAL
115BH34968X-RAY DIFFRACTION5.494TORSIONAL
116BJ34968X-RAY DIFFRACTION5.494TORSIONAL
117BL34968X-RAY DIFFRACTION5.494TORSIONAL
118BN34968X-RAY DIFFRACTION5.494TORSIONAL
119BP34968X-RAY DIFFRACTION5.494TORSIONAL
120BR34968X-RAY DIFFRACTION5.494TORSIONAL
121BT34968X-RAY DIFFRACTION5.494TORSIONAL
122BV34968X-RAY DIFFRACTION5.494TORSIONAL
123CB34968X-RAY DIFFRACTION5.494TORSIONAL
124CD34968X-RAY DIFFRACTION5.494TORSIONAL
125CF34968X-RAY DIFFRACTION5.494TORSIONAL
126CH34968X-RAY DIFFRACTION5.494TORSIONAL
127CJ34968X-RAY DIFFRACTION5.494TORSIONAL
128CL34968X-RAY DIFFRACTION5.494TORSIONAL
129CN34968X-RAY DIFFRACTION5.494TORSIONAL
130CP34968X-RAY DIFFRACTION5.494TORSIONAL
131CR34968X-RAY DIFFRACTION5.494TORSIONAL
132CT34968X-RAY DIFFRACTION5.494TORSIONAL
133CV34968X-RAY DIFFRACTION5.494TORSIONAL
134DB34968X-RAY DIFFRACTION5.494TORSIONAL
135DD34968X-RAY DIFFRACTION5.494TORSIONAL
136DF34968X-RAY DIFFRACTION5.494TORSIONAL
137DH34968X-RAY DIFFRACTION5.494TORSIONAL
138DJ34968X-RAY DIFFRACTION5.494TORSIONAL
139DL34968X-RAY DIFFRACTION5.494TORSIONAL
140DN34968X-RAY DIFFRACTION5.494TORSIONAL
141DP34968X-RAY DIFFRACTION5.494TORSIONAL
142DR34968X-RAY DIFFRACTION5.494TORSIONAL
143DT34968X-RAY DIFFRACTION5.494TORSIONAL
144DV34968X-RAY DIFFRACTION5.494TORSIONAL
21AA45663X-RAY DIFFRACTION5.494TORSIONAL
22AC45663X-RAY DIFFRACTION5.494TORSIONAL
23AE45663X-RAY DIFFRACTION5.494TORSIONAL
24AG45663X-RAY DIFFRACTION5.494TORSIONAL
25AI45663X-RAY DIFFRACTION5.494TORSIONAL
26AK45663X-RAY DIFFRACTION5.494TORSIONAL
27AM45663X-RAY DIFFRACTION5.494TORSIONAL
28AO45663X-RAY DIFFRACTION5.494TORSIONAL
29AQ45663X-RAY DIFFRACTION5.494TORSIONAL
210AS45663X-RAY DIFFRACTION5.494TORSIONAL
211AU45663X-RAY DIFFRACTION5.494TORSIONAL
212BA45663X-RAY DIFFRACTION5.494TORSIONAL
213BC45663X-RAY DIFFRACTION5.494TORSIONAL
214BE45663X-RAY DIFFRACTION5.494TORSIONAL
215BG45663X-RAY DIFFRACTION5.494TORSIONAL
216BI45663X-RAY DIFFRACTION5.494TORSIONAL
217BK45663X-RAY DIFFRACTION5.494TORSIONAL
218BM45663X-RAY DIFFRACTION5.494TORSIONAL
219BO45663X-RAY DIFFRACTION5.494TORSIONAL
220BQ45663X-RAY DIFFRACTION5.494TORSIONAL
221BS45663X-RAY DIFFRACTION5.494TORSIONAL
222BU45663X-RAY DIFFRACTION5.494TORSIONAL
223CA45663X-RAY DIFFRACTION5.494TORSIONAL
224CC45663X-RAY DIFFRACTION5.494TORSIONAL
225CE45663X-RAY DIFFRACTION5.494TORSIONAL
226CG45663X-RAY DIFFRACTION5.494TORSIONAL
227CI45663X-RAY DIFFRACTION5.494TORSIONAL
228CK45663X-RAY DIFFRACTION5.494TORSIONAL
229CM45663X-RAY DIFFRACTION5.494TORSIONAL
230CO45663X-RAY DIFFRACTION5.494TORSIONAL
231CQ45663X-RAY DIFFRACTION5.494TORSIONAL
232CS45663X-RAY DIFFRACTION5.494TORSIONAL
233CU45663X-RAY DIFFRACTION5.494TORSIONAL
234DA45663X-RAY DIFFRACTION5.494TORSIONAL
235DC45663X-RAY DIFFRACTION5.494TORSIONAL
236DE45663X-RAY DIFFRACTION5.494TORSIONAL
237DG45663X-RAY DIFFRACTION5.494TORSIONAL
238DI45663X-RAY DIFFRACTION5.494TORSIONAL
239DK45663X-RAY DIFFRACTION5.494TORSIONAL
240DM45663X-RAY DIFFRACTION5.494TORSIONAL
241DO45663X-RAY DIFFRACTION5.494TORSIONAL
242DQ45663X-RAY DIFFRACTION5.494TORSIONAL
243DS45663X-RAY DIFFRACTION5.494TORSIONAL
244DU45663X-RAY DIFFRACTION5.494TORSIONAL
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.98540.0720.13891.24540.6610.9472-0.16150.2632-0.0224-0.39990.153-0.3930.15210.18420.05471.0087-0.08020.14910.607-0.05790.403316.8853102.3193-13.0604
20.8263-0.1922-0.33661.00280.05231.0570.005-0.43620.40191.3419-0.2182-0.39850.32950.08180.10970.885-0.1168-0.07640.6491-0.07520.521418.4337115.864814.3819
30.72270.0326-0.07231.01080.26750.8612-0.2280.2567-0.07150.04520.00891.62540.4737-0.80930.19740.841-0.1814-0.01370.77720.02381.6541-18.9879124.14311.7224
41.19540.13620.20511.5764-0.02661.0732-0.12850.1642-0.1468-1.30910.0980.11030.00350.00760.04240.7316-0.1123-0.02950.4131-0.03250.49385.263136.4354-12.7847
50.95450.0402-0.17931.0571-0.2550.8318-0.1969-0.5603-0.11350.75430.3032-0.4540.08330.0796-0.07250.57510.1663-0.18680.78550.0390.479410.4327148.711725.2127
61.0421-0.20640.19670.75070.10870.7722-0.1473-0.3291-0.3567-0.28230.35190.67270.1884-0.4422-0.11110.28230.0089-0.08040.55690.12720.3882-13.1203159.19588.7766
70.8113-0.26190.26030.91390.08861.10480.21810.1846-0.2039-1.0135-0.1004-0.8816-0.01280.3636-0.14150.8192-0.0120.2240.4766-0.16350.268920.5246168.0669-14.3454
81.0696-0.0794-0.20190.85030.00950.8218-0.1431-0.46350.39240.21290.1479-0.1958-0.03670.19910.00490.34940.0051-0.04970.4554-0.10890.339714.5591182.28912.1147
90.60430.36170.20630.8963-0.16261.01470.05680.0862-0.1153-0.70610.9481.48160.3974-0.5041-0.26090.7592-0.6921-0.64760.77950.56341.248-17.5267188.1411-10.5941
100.9913-0.07930.22372.0337-0.28680.70340.14750.0857-0.1384-0.9184-0.0493-0.53460.23930.1255-0.07430.5274-0.0568-0.07440.5204-0.03260.278.4191202.4693-17.3547
111.0914-0.1279-0.01380.7373-0.34210.8863-0.0343-0.23420.05370.17280.07090.05660.0738-0.0878-0.01040.16710.0503-0.01070.4579-0.03760.18672.0012213.649221.0477
120.6416-0.2939-0.00221.48030.00720.77680.47770.41690.0428-0.5194-0.39261.005-0.1211-0.6435-0.0496-0.25950.1939-0.38420.87580.0420.1193-16.9283223.151-1.1242
130.8598-0.26960.17791.4123-0.12180.678-0.02-0.1665-0.1671-0.83140.0683-0.0548-0.07660.54370.0590.5736-0.11510.18430.7147-0.08120.422221.2101235.2201-12.409
141.4048-0.12290.10061.1988-0.10.8454-0.2127-0.3506-0.23390.28830.00660.147-0.43490.30240.01920.3454-0.049-0.08180.5443-0.00870.41236.4363248.163911.208
150.72510.3661-0.18720.73150.08780.7970.12020.3444-0.0785-0.25950.09770.23720.116-0.3706-0.08651.12720.0241-0.59730.825-0.00230.3573-17.8561254.1275-19.1845
160.75230.10490.1581.021-0.01740.61120.30770.13330.2327-0.4260.0739-0.7994-0.07590.3328-0.23161.2295-0.0429-0.11510.7344-0.14310.03379.0614269.0086-18.4859
171.06660.41030.18340.9543-0.25760.9088-0.4526-0.82730.2101-0.6643-0.71290.07660.946-0.55550.11331.3025-0.20150.99930.21831.0262-2.0896-9.8532279.211815.2609
180.52780.1664-0.37091.35330.10880.69190.17240.47630.0841-0.7662-0.09870.70920.2908-0.4059-0.09241.05470.2381-0.08130.74590.0420.4414-20.0219289.8767-11.8239
190.8379-0.1536-0.22550.71670.15940.8636-0.1363-0.19090.2893-0.18750.1399-0.21320.03270.5071-0.14220.90720.0810.27960.69270.14270.507419.9352301.2232-9.2014
200.97-0.003-0.20770.7522-00.6087-0.079-0.2367-0.13970.91840.16810.2545-0.16660.35890.00730.81150.00540.82090.41340.554-0.7994-1.2508313.20369.3126
210.47660.1769-0.16270.57810.10740.8855-0.05490.5174-0.0213-1.2523-0.0730.16060.6267-0.3840.11541.60990.0779-0.07381.2124-0.06060.6669-15.348323.208-26.0497
220.46080.0421-0.05721.1555-0.51110.97470.01350.087-0.1881-0.3195-0.5164-1.216-0.3250.63120.16221.54280.32860.89460.84120.32330.156910.5757335.9306-16.3817
230.7028-0.2706-0.19920.93660.0250.54470.02160.39410.2858-0.5306-0.03-0.62170.0711-0.05640.02931.17070.18620.29060.68230.00690.828678.1914330.58-16.9051
241.10430.1125-0.23841.3879-0.06961.35750.2709-0.02110.1537-0.2673-0.07540.9228-0.4075-0.0977-0.18050.83560.1972-0.0120.4839-0.02550.514755.2352318.9142-0.3401
250.9616-0.0228-0.08420.7131-0.0120.7590.2895-0.51560.20270.96260.2236-0.72660.17080.3778-0.30831.46990.1399-0.46240.9233-0.23611.108187.6311308.977920.6541
261.05940.1084-0.04940.84050.10450.6698-0.26590.3084-0.0857-0.55420.3733-1.2378-0.32470.13890.00260.91940.14690.10380.4675-0.18710.965682.8597296.0189-6.6127
270.7634-0.04170.2380.6136-0.26810.9034-0.2557-0.3272-0.14680.67980.12510.5142-0.289-0.63350.08590.89460.17760.33850.72430.02650.791448.7035287.360813.1787
280.45790.23630.1890.76190.01750.8227-0.0762-0.61220.04961.3979-0.2463-0.85460.22390.56230.25251.34760.1247-0.35830.92240.07980.737975.6458274.223921.0664
290.9263-0.0176-0.12841.0562-0.21770.7620.01750.20430.1964-0.25620.04370.16160.0933-0.1472-0.06490.34990.01060.09390.43750.12760.29870.7332265.806-18.7203
300.50810.2597-0.05821.0910.06521.02430.10240.10120.23260.6304-0.07411.2624-0.1238-0.1336-0.02840.54720.01890.41720.42970.03980.604552.2037253.41152.3046
310.69240.48220.26241.0846-0.10671.1232-0.234-0.37140.22871.1206-0.2862-0.5004-0.63030.65920.19910.7943-0.1479-0.39890.5776-0.08250.682189.148241.33412.7659
321.0536-0.32470.01440.92770.31860.7321-0.05840.19760.201-0.41520.001-0.42970.01920.02920.05680.4188-0.00290.12070.44250.04430.318175.8733230.4554-12.767
330.84520.01190.12380.47710.19580.5025-0.0679-0.68380.43331.19950.16050.7440.1201-0.25460.03510.6534-0.49461.6360.45620.34910.126849.3345222.544318.616
340.96570.1456-0.20610.91920.21111.11820.6687-0.1911-0.20140.99530.0862-1.31770.41870.2967-0.07851.2382-0.21750.27860.3950.2407-0.496176.2227207.883215.3595
351.55970.0597-0.33871.1046-0.33611.01020.3450.1717-0.1802-0.1636-0.02860.2702-0.2335-0.074-0.28560.4433-0.0494-0.08530.52310.08350.463656.4811201.6314-18.1215
360.94910.15830.00380.6156-0.28610.98830.1889-0.0043-0.0220.38270.19650.9467-0.2109-0.2463-0.24420.4385-0.02430.15330.5210.09920.70746.9076187.76477.7061
370.50480.0534-0.01670.4922-0.07880.59650.1387-0.0299-0.1410.0688-0.3246-0.4012-0.36840.37660.05650.0982-0.0386-0.24690.52170.12090.869986.9637177.1173.0712
381.10450.0394-0.08880.7877-0.21650.58180.06990.3488-0.0483-0.3935-0.0070.34610.2142-0.3155-0.03440.3899-0.0538-0.10580.4893-0.00970.429665.5613167.0925-16.4139
390.9102-0.2567-0.1011.14950.24090.9641-0.11950.00510.12890.59350.09140.41760.1763-0.07840.11310.53320.05750.18870.47960.14450.895353.5324153.698517.965
400.83530.2059-0.21610.7579-0.06361.0114-0.041-0.0440.14160.18230.206-0.74020.24940.2825-0.09740.40460.0483-0.14770.4850.06940.823179.1462142.06446.367
410.78980.05170.24950.8043-0.07560.659-0.04140.98070.0734-1.00970.00070.6522-0.0031-0.23870.07921.2027-0.0285-0.55491.1362-0.04331.174352.5695134.649-22.5181
420.86450.05010.31450.86930.14390.50580.0783-0.1705-0.23950.21120.00110.96990.3036-0.4744-0.09690.7092-0.20820.13360.6340.04031.305950.4389119.93234.3256
430.85960.2070.23050.86240.40120.88340.110.16460.2446-0.48690.0146-1.0476-0.19650.2715-0.11270.9228-0.12350.26210.5015-0.05111.260888.7974111.3323-7.5744
440.7101-0.06890.03680.98990.18120.9279-0.06210.49890.1158-1.2747-0.38140.61190.1883-0.39610.36831.25120.027-0.13230.7103-0.09920.786664.621599.5699-22.5929
451.17410.4926-0.31332.37660.1131.4383-0.45530.66140.1471-2.52640.6025-0.25090.8625-0.0083-0.08081.4964-0.14410.14220.68340.02490.7501-16.48331.453144.8971
460.83130.1711-0.01410.9844-0.02360.79410.06230.0282-0.1805-1.00940.56291.8125-0.0355-0.3305-0.21250.16250.666-1.5168-0.25551.09641.556-40.8539318.303857.7593
471.9523-0.0986-0.28361.06830.31590.810.1246-0.58990.50190.9420.2691-0.8208-0.08070.3215-0.29930.91010.1463-0.25480.76-0.20070.8505-12.3198307.810583.209
480.6619-0.16010.42321.36160.15560.64110.27010.7854-0.1536-2.0264-0.4081-0.98930.12570.01150.0241.40990.33810.06580.7986-0.14140.743-12.0013296.366154.6774
490.8789-0.15280.30990.77260.34560.9486-0.3205-0.25061.0740.8737-0.31271.37360.18-0.64470.175-2.88071.7307-0.2789-0.28720.26811.0238-49.2144286.62369.4325
500.95170.12650.18181.15260.42570.8988-0.0649-0.29150.17061.0842-0.2107-1.15240.16580.20180.11620.44420.1201-0.17580.59820.15560.6934-23.4295273.714880.234
510.853-0.3518-0.05391.28130.14010.56330.32090.21370.2577-1.6871-0.2774-0.7378-0.1607-0.012-0.02180.6785-0.01070.40110.51150.14050.5326-23.385265.869240.9734
520.5856-0.08910.05421.6629-0.12831.23080.1175-0.1281-0.03750.18390.3291.4285-0.4188-0.0389-0.1257-0.27060.1271-0.09940.46940.19310.3048-44.2884252.787958.9141
531.22880.4581-0.34211.62840.16130.62970.2274-0.14640.15790.5434-0.0982-0.3389-0.04130.2126-0.04460.23820.0134-0.08740.4565-0.00580.2616-10.0345241.11775.319
540.9381-0.18970.09730.8393-0.00120.43230.21210.871-0.2876-1.459-0.00130.04490.25550.3295-0.0073-0.38840.22760.37690.6878-0.05870.1251-17.9763230.828147.3437
551.0787-0.3191-0.14240.75550.07350.6397-0.5852-0.4812-0.37340.43570.66450.81070.7238-0.4137-0.0529-0.49290.05520.34420.56310.32330.7246-49.3829221.249473.0175
561.040.1829-0.2390.91330.0681.12050.269-0.0076-0.49550.25590.0509-0.42990.37580.1172-0.03020.2315-0.0581-0.03280.25590.15770.2827-22.2018207.285874.6329
570.9234-0.09030.03040.8846-0.0720.8157-0.28190.7385-0.531-0.1499-0.08570.1971-0.68290.54460.20030.8308-0.5458-0.01750.94240.09920.514-34.2112200.717437.65
580.90030.19890.30191.0482-0.07341.0124-0.4056-0.2596-0.7151-0.41410.29820.306-0.49850.00970.07490.4251-0.3045-0.13390.60210.01410.7745-48.8411186.779760.8467
590.98020.0303-0.07460.84090.55230.9015-0.09010.2796-0.52550.03420.3635-1.08530.00990.5749-0.22620.7208-0.09260.08930.6946-0.35651.5787-10.5149175.785765.7458
600.2473-0.1213-0.05540.6453-0.05060.37620.01320.5522-0.4096-1.1622-0.19360.0748-0.0718-0.05660.17131.124-0.10530.38950.9651-0.45741.382-26.6042165.459441.4979
610.9877-0.29590.11241.21480.30911.50780.2434-0.4920.40890.58890.54310.003-0.2571-0.2315-0.28760.91690.24130.43080.5754-0.05540.4672-48.1771154.318974.5731
621.33610.1134-0.21930.3839-0.19480.58440.2794-0.08520.24490.20240.3037-1.4484-0.07450.5325-0.37590.61890.02350.08030.6357-0.36981.1078-21.1513141.383168.6484
630.73440.13050.0371.19680.11421.17470.10460.7885-0.0163-1.25130.30460.1317-0.6375-0.2561-0.40011.3136-0.1076-0.08120.93840.0180.5343-42.5133.993235.6845
640.66710.18670.50352.3922-0.42871.5375-0.07660.0839-0.09870.5550.20591.1355-0.4047-0.4986-0.07180.24590.0888-0.12840.5182-0.00860.7317-50.0974120.470962.0809
650.91730.1805-0.21280.90790.29560.58720.42440.1267-0.33810.13730.7466-1.5741-0.34910.6922-0.4230.2154-0.6688-0.25570.2747-1.0222.7306-11.7638109.892556.3378
660.8319-0.0477-0.08580.76190.07760.5221-0.38690.4701-0.3765-1.55960.1168-0.17290.2181-0.13770.21141.023-0.09820.14720.8054-0.40510.9387-34.033598.275138.2616
671.17260.17-0.20731.15310.20480.77260.0033-0.03320.2966-0.82490.1196-1.1904-0.12810.6913-0.00780.724-0.12550.31130.7245-0.05610.980755.7157101.355350.1334
681.00190.1767-0.22331.1622-0.03840.3393-0.2894-0.4680.24971.050.0263-0.6183-0.16590.62350.12460.9388-0.0888-0.32740.8584-0.0810.851252.1141113.456878.4936
690.9627-0.0067-0.24710.7732-0.04771.33370.05670.03080.2713-0.4119-0.29871.2270.2102-0.03160.04770.4037-0.173-0.09160.3283-0.17921.13617.543122.628858.2061
700.835-0.10880.11021.61530.38210.84690.174-0.10160.2007-0.96610.0801-0.4799-0.46950.5121-0.06240.5985-0.2668-0.03850.5728-0.04440.621544.0986135.189650.228
710.93570.19690.01680.6854-0.37070.8247-0.1309-0.463-0.12840.531-0.2727-0.03860.4411-0.28720.3061.114-0.14430.14460.8736-0.04180.687140.331146.404688.2928
720.6719-0.0571-0.04710.56970.0271.21840.3880.02810.3058-0.284-0.11070.9230.3544-0.5401-0.17150.8757-0.27170.10720.7311-0.25031.279321.4867157.725166.9514
730.8985-0.2412-0.12491.13580.43431.2397-0.11190.0696-0.4032-0.2076-0.054-0.2174-0.10050.15990.13320.3744-0.0070.05810.398-0.08850.710158.7742166.900253.2475
740.9526-0.108-0.29311.65620.23140.5204-0.1949-0.1395-0.07660.9403-0.301-0.3836-0.2559-0.14140.27760.483-0.0653-0.19330.438-0.05820.699347.2991180.596278.2176
750.79550.0621-0.10010.90360.40150.65441.04020.912-1.11650.2024-0.1940.03010.2966-0.6751-0.1545-0.0916-0.7092-1.18310.2851-0.75740.866120.9022188.272749.6856
761.2189-0.1364-0.05342.63040.27530.6280.24560.3501-0.3758-0.6666-0.0363-1.2728-0.3244-0.1016-0.09180.34910.1534-0.13760.60490.01110.54248.6526201.460248.5999
770.95660.05670.07410.7764-0.07580.495-0.0715-0.21070.21340.29360.1544-0.03350.4803-0.0694-0.05290.51350.0431-0.0920.4048-0.00160.175933.012211.779685.2301
780.713-0.10450.04231.671-0.23030.97790.01150.33760.1981-0.3050.20421.02190.5285-0.367-0.10010.17960.0197-0.13520.56430.17340.079420.8806222.696159.4646
790.8532-0.3430.0680.84260.02170.8923-0.80640.6182-0.6491-0.39650.1871-0.72530.34570.58570.1693-3.12171.280.63420.2908-0.35840.998758.4812234.071157.4633
800.97610.2604-0.11821.1867-0.3180.8147-0.0562-0.2568-0.18461.8437-0.0781-0.3016-0.12750.05090.00850.27410.1429-0.24510.43990.10050.334439.7595247.449177.6684
810.56870.28440.09830.74120.0070.6756-0.43920.1856-0.0623-0.78640.3960.61880.2158-0.089-0.03030.3230.0055-0.34180.60590.12780.407421.1326252.911541.5042
820.66550.17450.10771.44010.07930.89240.09930.1358-0.1895-0.4215-0.0395-0.88050.0109-0.0017-0.00010.24820.00720.00540.52530.02590.264147.4918267.068147.6856
830.96740.2004-0.17020.8918-0.42330.7934-0.2441-0.72990.47761.2925-0.00170.23160.0194-0.3180.04980.9914-0.19660.87580.19620.66350.062122.8217278.247776.7803
840.57410.109-0.12470.85590.14020.87770.02690.26440.3204-0.68260.04511.3301-0.083-0.1708-0.06020.4260.126-0.17840.45290.1940.711818.4046288.964648.3838
850.5769-0.1226-0.09040.8482-0.07340.7671-0.1058-0.0230.07870.25230.2406-1.20790.03730.3640.0690.1006-0.05940.00480.6583-0.10980.58657.95298.668558.335
860.926-0.3119-0.05881.16810.0830.89930.0112-0.2854-0.03861.34410.0130.1481-0.2690.00350.02890.80310.09340.01370.463-0.04130.304734.3616311.775172.2767
870.63170.2703-0.22041.38920.26631.14840.3105-0.0306-0.1728-1.1308-0.25170.22630.5921-0.9182-0.03761.3563-0.3091-0.26190.91230.11760.585428.3363320.496534.3473
880.5078-0.2372-0.0091.60620.07521.3721-0.0372-0.01750.0978-0.61160.1396-1.3131-0.05810.3891-0.00170.6243-0.15010.16690.53420.08780.740451.7829333.596149.1698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'AA' and resid 16 through 238)AA16 - 238
2X-RAY DIFFRACTION2(chain 'AB' and resid 1 through 163)AB1 - 163
3X-RAY DIFFRACTION3(chain 'AC' and resid 16 through 238)AC16 - 238
4X-RAY DIFFRACTION4(chain 'AD' and resid 1 through 163)AD1 - 163
5X-RAY DIFFRACTION5(chain 'AE' and resid 16 through 238)AE16 - 238
6X-RAY DIFFRACTION6(chain 'AF' and resid 1 through 163)AF1 - 163
7X-RAY DIFFRACTION7(chain 'AG' and resid 16 through 238)AG16 - 238
8X-RAY DIFFRACTION8(chain 'AH' and resid 1 through 163)AH1 - 163
9X-RAY DIFFRACTION9(chain 'AI' and resid 16 through 238)AI16 - 238
10X-RAY DIFFRACTION10(chain 'AJ' and resid 1 through 163)AJ1 - 163
11X-RAY DIFFRACTION11(chain 'AK' and resid 16 through 238)AK16 - 238
12X-RAY DIFFRACTION12(chain 'AL' and resid 1 through 163)AL1 - 163
13X-RAY DIFFRACTION13(chain 'AM' and resid 16 through 238)AM16 - 238
14X-RAY DIFFRACTION14(chain 'AN' and resid 1 through 163)AN1 - 163
15X-RAY DIFFRACTION15(chain 'AO' and resid 16 through 238)AO16 - 238
16X-RAY DIFFRACTION16(chain 'AP' and resid 1 through 163)AP1 - 163
17X-RAY DIFFRACTION17(chain 'AQ' and resid 16 through 238)AQ16 - 238
18X-RAY DIFFRACTION18(chain 'AR' and resid 1 through 163)AR1 - 163
19X-RAY DIFFRACTION19(chain 'AS' and resid 16 through 238)AS16 - 238
20X-RAY DIFFRACTION20(chain 'AT' and resid 1 through 163)AT1 - 163
21X-RAY DIFFRACTION21(chain 'AU' and resid 16 through 238)AU16 - 238
22X-RAY DIFFRACTION22(chain 'AV' and resid 1 through 163)AV1 - 163
23X-RAY DIFFRACTION23(chain 'BA' and resid 16 through 238)BA16 - 238
24X-RAY DIFFRACTION24(chain 'BB' and resid 1 through 163)BB1 - 163
25X-RAY DIFFRACTION25(chain 'BC' and resid 16 through 238)BC16 - 238
26X-RAY DIFFRACTION26(chain 'BD' and resid 1 through 163)BD1 - 163
27X-RAY DIFFRACTION27(chain 'BE' and resid 16 through 238)BE16 - 238
28X-RAY DIFFRACTION28(chain 'BF' and resid 1 through 163)BF1 - 163
29X-RAY DIFFRACTION29(chain 'BG' and resid 16 through 238)BG16 - 238
30X-RAY DIFFRACTION30(chain 'BH' and resid 1 through 163)BH1 - 163
31X-RAY DIFFRACTION31(chain 'BI' and resid 16 through 238)BI16 - 238
32X-RAY DIFFRACTION32(chain 'BJ' and resid 1 through 163)BJ1 - 163
33X-RAY DIFFRACTION33(chain 'BK' and resid 16 through 238)BK16 - 238
34X-RAY DIFFRACTION34(chain 'BL' and resid 1 through 163)BL1 - 163
35X-RAY DIFFRACTION35(chain 'BM' and resid 16 through 238)BM16 - 238
36X-RAY DIFFRACTION36(chain 'BN' and resid 1 through 163)BN1 - 163
37X-RAY DIFFRACTION37(chain 'BO' and resid 16 through 238)BO16 - 238
38X-RAY DIFFRACTION38(chain 'BP' and resid 1 through 163)BP1 - 163
39X-RAY DIFFRACTION39(chain 'BQ' and resid 16 through 238)BQ16 - 238
40X-RAY DIFFRACTION40(chain 'BR' and resid 1 through 163)BR1 - 163
41X-RAY DIFFRACTION41(chain 'BS' and resid 16 through 238)BS16 - 238
42X-RAY DIFFRACTION42(chain 'BT' and resid 1 through 163)BT1 - 163
43X-RAY DIFFRACTION43(chain 'BU' and resid 16 through 238)BU16 - 238
44X-RAY DIFFRACTION44(chain 'BV' and resid 1 through 163)BV1 - 163
45X-RAY DIFFRACTION45(chain 'CA' and resid 16 through 238)CA16 - 238
46X-RAY DIFFRACTION46(chain 'CB' and resid 1 through 163)CB1 - 163
47X-RAY DIFFRACTION47(chain 'CC' and resid 16 through 238)CC16 - 238
48X-RAY DIFFRACTION48(chain 'CD' and resid 1 through 163)CD1 - 163
49X-RAY DIFFRACTION49(chain 'CE' and resid 16 through 238)CE16 - 238
50X-RAY DIFFRACTION50(chain 'CF' and resid 1 through 163)CF1 - 163
51X-RAY DIFFRACTION51(chain 'CG' and resid 16 through 238)CG16 - 238
52X-RAY DIFFRACTION52(chain 'CH' and resid 1 through 163)CH1 - 163
53X-RAY DIFFRACTION53(chain 'CI' and resid 16 through 238)CI16 - 238
54X-RAY DIFFRACTION54(chain 'CJ' and resid 1 through 163)CJ1 - 163
55X-RAY DIFFRACTION55(chain 'CK' and resid 16 through 238)CK16 - 238
56X-RAY DIFFRACTION56(chain 'CL' and resid 1 through 163)CL1 - 163
57X-RAY DIFFRACTION57(chain 'CM' and resid 16 through 238)CM16 - 238
58X-RAY DIFFRACTION58(chain 'CN' and resid 1 through 163)CN1 - 163
59X-RAY DIFFRACTION59(chain 'CO' and resid 16 through 238)CO16 - 238
60X-RAY DIFFRACTION60(chain 'CP' and resid 1 through 163)CP1 - 163
61X-RAY DIFFRACTION61(chain 'CQ' and resid 16 through 238)CQ16 - 238
62X-RAY DIFFRACTION62(chain 'CR' and resid 1 through 163)CR1 - 163
63X-RAY DIFFRACTION63(chain 'CS' and resid 16 through 238)CS16 - 238
64X-RAY DIFFRACTION64(chain 'CT' and resid 1 through 163)CT1 - 163
65X-RAY DIFFRACTION65(chain 'CU' and resid 16 through 238)CU16 - 238
66X-RAY DIFFRACTION66(chain 'CV' and resid 1 through 163)CV1 - 163
67X-RAY DIFFRACTION67(chain 'DA' and resid 16 through 238)DA16 - 238
68X-RAY DIFFRACTION68(chain 'DB' and resid 1 through 163)DB1 - 163
69X-RAY DIFFRACTION69(chain 'DC' and resid 16 through 238)DC16 - 238
70X-RAY DIFFRACTION70(chain 'DD' and resid 1 through 163)DD1 - 163
71X-RAY DIFFRACTION71(chain 'DE' and resid 16 through 238)DE16 - 238
72X-RAY DIFFRACTION72(chain 'DF' and resid 1 through 163)DF1 - 163
73X-RAY DIFFRACTION73(chain 'DG' and resid 16 through 238)DG16 - 238
74X-RAY DIFFRACTION74(chain 'DH' and resid 1 through 163)DH1 - 163
75X-RAY DIFFRACTION75(chain 'DI' and resid 16 through 238)DI16 - 238
76X-RAY DIFFRACTION76(chain 'DJ' and resid 1 through 163)DJ1 - 163
77X-RAY DIFFRACTION77(chain 'DK' and resid 16 through 238)DK16 - 238
78X-RAY DIFFRACTION78(chain 'DL' and resid 1 through 163)DL1 - 163
79X-RAY DIFFRACTION79(chain 'DM' and resid 16 through 238)DM16 - 238
80X-RAY DIFFRACTION80(chain 'DN' and resid 1 through 163)DN1 - 163
81X-RAY DIFFRACTION81(chain 'DO' and resid 16 through 238)DO16 - 238
82X-RAY DIFFRACTION82(chain 'DP' and resid 1 through 163)DP1 - 163
83X-RAY DIFFRACTION83(chain 'DQ' and resid 16 through 238)DQ16 - 238
84X-RAY DIFFRACTION84(chain 'DR' and resid 1 through 163)DR1 - 163
85X-RAY DIFFRACTION85(chain 'DS' and resid 16 through 238)DS16 - 238
86X-RAY DIFFRACTION86(chain 'DT' and resid 1 through 163)DT1 - 163
87X-RAY DIFFRACTION87(chain 'DU' and resid 16 through 238)DU16 - 238
88X-RAY DIFFRACTION88(chain 'DV' and resid 1 through 163)DV1 - 163

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more