[English] 日本語
Yorodumi
- PDB-6r7d: Crystal structure of LTC4S in complex with AZ13690257 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r7d
TitleCrystal structure of LTC4S in complex with AZ13690257
ComponentsLeukotriene C4 synthase
KeywordsMEMBRANE PROTEIN / Inhibitor / arachidonic acid cascade / cysteinyl leukotrienes
Function / homology
Function and homology information


Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process ...Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process / glutathione peroxidase activity / nuclear outer membrane / long-chain fatty acid biosynthetic process / glutathione transferase activity / enzyme activator activity / nuclear envelope / nuclear membrane / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / identical protein binding
Similarity search - Function
5-lipoxygenase-activating protein / FLAP/GST2/LTC4S, conserved site / FLAP/GST2/LTC4S family signature. / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JUQ / NICKEL (II) ION / PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKack, H. / Ek, M.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of the Oral Leukotriene C4 Synthase Inhibitor (1S,2S)-2-({5-[(5-Chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic Acid ...Title: Discovery of the Oral Leukotriene C4 Synthase Inhibitor (1S,2S)-2-({5-[(5-Chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic Acid (AZD9898) as a New Treatment for Asthma.
Authors: Munck Af Rosenschold, M. / Johannesson, P. / Nikitidis, A. / Tyrchan, C. / Chang, H.F. / Ronn, R. / Chapman, D. / Ullah, V. / Nikitidis, G. / Glader, P. / Kack, H. / Bonn, B. / Wagberg, F. / ...Authors: Munck Af Rosenschold, M. / Johannesson, P. / Nikitidis, A. / Tyrchan, C. / Chang, H.F. / Ronn, R. / Chapman, D. / Ullah, V. / Nikitidis, G. / Glader, P. / Kack, H. / Bonn, B. / Wagberg, F. / Bjorkstrand, E. / Andersson, U. / Swedin, L. / Rohman, M. / Andreasson, T. / Bergstrom, E.L. / Jiang, F. / Zhou, X.H. / Lundqvist, A.J. / Malmberg, A. / Ek, M. / Gordon, E. / Pettersen, A. / Ripa, L. / Davis, A.M.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 13, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leukotriene C4 synthase
B: Leukotriene C4 synthase
C: Leukotriene C4 synthase
D: Leukotriene C4 synthase
E: Leukotriene C4 synthase
F: Leukotriene C4 synthase
G: Leukotriene C4 synthase
H: Leukotriene C4 synthase
I: Leukotriene C4 synthase
J: Leukotriene C4 synthase
K: Leukotriene C4 synthase
L: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,80776
Polymers209,79112
Non-polymers17,01664
Water1,74797
1
A: Leukotriene C4 synthase
B: Leukotriene C4 synthase
C: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49026
Polymers52,4483
Non-polymers6,04223
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-71 kcal/mol
Surface area21120 Å2
MethodPISA
2
D: Leukotriene C4 synthase
E: Leukotriene C4 synthase
F: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58018
Polymers52,4483
Non-polymers4,13215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint-75 kcal/mol
Surface area21180 Å2
MethodPISA
3
G: Leukotriene C4 synthase
H: Leukotriene C4 synthase
I: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,61315
Polymers52,4483
Non-polymers3,16512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-71 kcal/mol
Surface area21800 Å2
MethodPISA
4
J: Leukotriene C4 synthase
K: Leukotriene C4 synthase
L: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,12517
Polymers52,4483
Non-polymers3,67814
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-62 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.591, 169.385, 174.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains A D
44Chains A E
55Chains A F
66Chains A G
77Chains A H
88Chains A I
99Chains A J
1010Chains A K
1111Chains A L
1212Chains B C
1313Chains B D
1414Chains B E
1515Chains B F
1616Chains B G
1717Chains B H
1818Chains B I
1919Chains B J
2020Chains B K
2121Chains B L
2222Chains C D
2323Chains C E
2424Chains C F
2525Chains C G
2626Chains C H
2727Chains C I
2828Chains C J
2929Chains C K
3030Chains C L
3131Chains D E
3232Chains D F
3333Chains D G
3434Chains D H
3535Chains D I
3636Chains D J
3737Chains D K
3838Chains D L
3939Chains E F
4040Chains E G
4141Chains E H
4242Chains E I
4343Chains E J
4444Chains E K
4545Chains E L
4646Chains F G
4747Chains F H
4848Chains F I
4949Chains F J
5050Chains F K
5151Chains F L
5252Chains G H
5353Chains G I
5454Chains G J
5555Chains G K
5656Chains G L
5757Chains H I
5858Chains H J
5959Chains H K
6060Chains H L
6161Chains I J
6262Chains I K
6363Chains I L
6464Chains J K
6565Chains J L
6666Chains K L

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

-
Components

-
Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJKL

#1: Protein
Leukotriene C4 synthase / / LTC4 synthase / Leukotriene-C(4) synthase


Mass: 17482.621 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTC4S / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 160 molecules

#2: Chemical
ChemComp-JUQ / (1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid


Mass: 417.457 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H23N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#4: Chemical...
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C16H32O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: CaCl2, PEG400, Hepes

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.35→170 Å / Num. obs: 150050 / % possible obs: 99.2 % / Redundancy: 6.4 % / Net I/σ(I): 18.1
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 7388

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135 2015/10/01refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCV
Resolution: 2.35→121.534 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.286 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 7340 -random
Rwork0.2081 ---
all0.209 ---
obs-149953 99.957 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.673 Å2-0 Å2-0 Å2
2---0.176 Å20 Å2
3---0.849 Å2
Refinement stepCycle: LAST / Resolution: 2.35→121.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14126 0 928 97 15151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01915472
X-RAY DIFFRACTIONr_bond_other_d0.0160.0215356
X-RAY DIFFRACTIONr_angle_refined_deg2.2442.00820916
X-RAY DIFFRACTIONr_angle_other_deg2.018334886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41251778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.19919.871620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.445152126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.81115152
X-RAY DIFFRACTIONr_chiral_restr0.1390.22282
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02117138
X-RAY DIFFRACTIONr_gen_planes_other0.0130.023910
X-RAY DIFFRACTIONr_nbd_refined0.2230.27158
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.225352
X-RAY DIFFRACTIONr_nbtor_refined0.2060.214834
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.215604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2180
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2150.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3690.270
X-RAY DIFFRACTIONr_nbd_other0.4640.2231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.22
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.21
X-RAY DIFFRACTIONr_mcbond_it2.8853.537148
X-RAY DIFFRACTIONr_mcbond_other2.8833.537147
X-RAY DIFFRACTIONr_mcangle_it3.8295.2848914
X-RAY DIFFRACTIONr_mcangle_other3.8285.2848915
X-RAY DIFFRACTIONr_scbond_it4.8984.4198324
X-RAY DIFFRACTIONr_scbond_other4.8984.428325
X-RAY DIFFRACTIONr_scangle_it7.0626.32611930
X-RAY DIFFRACTIONr_scangle_other7.0626.32611931
X-RAY DIFFRACTIONr_lrange_it8.1530.57117257
X-RAY DIFFRACTIONr_lrange_other8.14130.56417252
X-RAY DIFFRACTIONr_ncsr_local_group_10.0620.0517396
X-RAY DIFFRACTIONr_ncsr_local_group_20.0760.0516862
X-RAY DIFFRACTIONr_ncsr_local_group_30.0410.0517512
X-RAY DIFFRACTIONr_ncsr_local_group_40.060.0517400
X-RAY DIFFRACTIONr_ncsr_local_group_50.0820.0516994
X-RAY DIFFRACTIONr_ncsr_local_group_60.0510.0517600
X-RAY DIFFRACTIONr_ncsr_local_group_70.0660.0517206
X-RAY DIFFRACTIONr_ncsr_local_group_80.0760.0516888
X-RAY DIFFRACTIONr_ncsr_local_group_90.0520.0517540
X-RAY DIFFRACTIONr_ncsr_local_group_100.0620.0517268
X-RAY DIFFRACTIONr_ncsr_local_group_110.0820.0516850
X-RAY DIFFRACTIONr_ncsr_local_group_120.0630.0517050
X-RAY DIFFRACTIONr_ncsr_local_group_130.0630.0517254
X-RAY DIFFRACTIONr_ncsr_local_group_140.0430.0517586
X-RAY DIFFRACTIONr_ncsr_local_group_150.0680.0517186
X-RAY DIFFRACTIONr_ncsr_local_group_160.0720.0517330
X-RAY DIFFRACTIONr_ncsr_local_group_170.0410.0517518
X-RAY DIFFRACTIONr_ncsr_local_group_180.0630.0517068
X-RAY DIFFRACTIONr_ncsr_local_group_190.0730.0517252
X-RAY DIFFRACTIONr_ncsr_local_group_200.030.0517546
X-RAY DIFFRACTIONr_ncsr_local_group_210.0690.0517024
X-RAY DIFFRACTIONr_ncsr_local_group_220.0770.0516890
X-RAY DIFFRACTIONr_ncsr_local_group_230.060.0517080
X-RAY DIFFRACTIONr_ncsr_local_group_240.0410.0517298
X-RAY DIFFRACTIONr_ncsr_local_group_250.0730.0516922
X-RAY DIFFRACTIONr_ncsr_local_group_260.0550.0517094
X-RAY DIFFRACTIONr_ncsr_local_group_270.0050.0517540
X-RAY DIFFRACTIONr_ncsr_local_group_280.0850.0516774
X-RAY DIFFRACTIONr_ncsr_local_group_290.0640.0517030
X-RAY DIFFRACTIONr_ncsr_local_group_300.0280.0517496
X-RAY DIFFRACTIONr_ncsr_local_group_310.0620.0517258
X-RAY DIFFRACTIONr_ncsr_local_group_320.0850.0517050
X-RAY DIFFRACTIONr_ncsr_local_group_330.0350.0517534
X-RAY DIFFRACTIONr_ncsr_local_group_340.0730.0517274
X-RAY DIFFRACTIONr_ncsr_local_group_350.0770.0516898
X-RAY DIFFRACTIONr_ncsr_local_group_360.0370.0517470
X-RAY DIFFRACTIONr_ncsr_local_group_370.0670.0517298
X-RAY DIFFRACTIONr_ncsr_local_group_380.0750.0516884
X-RAY DIFFRACTIONr_ncsr_local_group_390.0670.0517186
X-RAY DIFFRACTIONr_ncsr_local_group_400.0690.0517328
X-RAY DIFFRACTIONr_ncsr_local_group_410.0390.0517454
X-RAY DIFFRACTIONr_ncsr_local_group_420.060.0517102
X-RAY DIFFRACTIONr_ncsr_local_group_430.0660.0517310
X-RAY DIFFRACTIONr_ncsr_local_group_440.0360.0517476
X-RAY DIFFRACTIONr_ncsr_local_group_450.0660.0517056
X-RAY DIFFRACTIONr_ncsr_local_group_460.0790.0517044
X-RAY DIFFRACTIONr_ncsr_local_group_470.0670.0517326
X-RAY DIFFRACTIONr_ncsr_local_group_480.0410.0517312
X-RAY DIFFRACTIONr_ncsr_local_group_490.0890.0516866
X-RAY DIFFRACTIONr_ncsr_local_group_500.0760.0517324
X-RAY DIFFRACTIONr_ncsr_local_group_510.0490.0517280
X-RAY DIFFRACTIONr_ncsr_local_group_520.0730.0517166
X-RAY DIFFRACTIONr_ncsr_local_group_530.0730.0516936
X-RAY DIFFRACTIONr_ncsr_local_group_540.0410.0517584
X-RAY DIFFRACTIONr_ncsr_local_group_550.0690.0517196
X-RAY DIFFRACTIONr_ncsr_local_group_560.0720.0516924
X-RAY DIFFRACTIONr_ncsr_local_group_570.0560.0517112
X-RAY DIFFRACTIONr_ncsr_local_group_580.0710.0517128
X-RAY DIFFRACTIONr_ncsr_local_group_590.0330.0517688
X-RAY DIFFRACTIONr_ncsr_local_group_600.0620.0517082
X-RAY DIFFRACTIONr_ncsr_local_group_610.0840.0516790
X-RAY DIFFRACTIONr_ncsr_local_group_620.0650.0517060
X-RAY DIFFRACTIONr_ncsr_local_group_630.0280.0517522
X-RAY DIFFRACTIONr_ncsr_local_group_640.0680.0517204
X-RAY DIFFRACTIONr_ncsr_local_group_650.0830.0516766
X-RAY DIFFRACTIONr_ncsr_local_group_660.0710.0517004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.35-2.4110.3165550.281104201097699.99090.259
2.411-2.4770.2655850.248101431072999.99070.219
2.477-2.5490.2515140.21898921040899.98080.187
2.549-2.6270.2154800.2089635101151000.178
2.627-2.7130.2244790.1969332981499.96940.163
2.713-2.8090.2194570.1749068952699.98950.147
2.809-2.9150.1944670.181872791941000.154
2.915-3.0330.2084810.1828360884299.98870.157
3.033-3.1680.2244230.198063848799.98820.168
3.168-3.3230.2263590.1947774813599.97540.174
3.323-3.5020.1973970.1917338773699.98710.176
3.502-3.7150.2093260.1997014734299.97280.189
3.715-3.9710.2063000.195659368931000.188
3.971-4.2890.2172620.1966194645899.9690.192
4.289-4.6970.2082870.1915670596199.93290.193
4.697-5.2510.2222700.1945125539799.96290.197
5.251-6.0610.2432560.2384570482799.97930.234
6.061-7.4190.2471910.2273884407799.95090.231
7.419-10.4720.1851430.1683062321699.6580.188
10.472-121.5340.4071080.4061749188498.56690.385
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)
10.55750.7824-0.09671.8483-0.11791.11090.0539-0.0501-0.00990.2314-0.14610.13640.0406-0.10170.09220.1275-0.10680.11130.0989-0.08720.30614.089158.62332.6432
21.24850.62710.15641.92011.00380.93280.009-0.0092-0.03530.0555-0.0370.07790.14320.07170.02810.1342-0.04770.03670.0804-0.06310.241426.190247.734626.2295
31.99880.28470.02151.39470.00750.49350.11490.13140.0188-0.0982-0.13240.2470.0313-0.09910.01750.0745-0.04920.01030.1187-0.07950.255716.342857.801215.4036
41.1406-0.4129-0.46060.97330.81851.4830.19210.12510.0417-0.3049-0.19370.0834-0.1012-0.0320.00160.23370.10520.08320.1068-0.03620.173159.10883.8269-6.9582
51.8484-0.37-0.61080.4301-0.25680.88850.1157-0.0122-0.0613-0.1078-0.0879-0.051-0.03820.0421-0.02780.10470.01370.11360.0859-0.04260.209768.114270.81290.8535
60.92810.0562-0.80331.3164-0.0261.48130.16010.0410.2-0.0938-0.0058-0.1527-0.17710.0014-0.15430.1193-0.01190.13530.069-0.04830.201272.516387.38784.0413
70.7252-0.05720.66731.5202-0.37721.43090.042-0.0885-0.18070.09260.0165-0.12690.1821-0.1552-0.05850.10850.0155-0.0760.0582-0.01290.161-54.077668.06954.0322
81.4784-0.29740.510.81560.36271.7826-0.0135-0.34440.02050.2141-0.06430.12920.0321-0.14680.07780.1146-0.0419-0.01250.1853-0.0290.0762-67.049874.996363.2741
92.0703-0.15630.72170.5251-0.40610.86170.0372-0.07780.15070.1455-0.0574-0.13530.0044-0.0260.02020.10030.0081-0.11710.1052-0.04670.1944-53.762485.208756.99
100.80320.22680.13761.3883-0.18130.92920.05110.03590.1707-0.08770.02530.0255-0.1622-0.123-0.07640.13390.01430.1060.04240.07820.3365-35.570233.47358.5464
111.86890.6567-0.63191.82920.23030.50130.12840.051-0.0102-0.06180.0473-0.1523-0.15870.0563-0.17570.115-0.06690.08170.09140.02220.2871-23.129826.053548.9176
120.95060.0826-0.44541.88350.44931.66450.0576-0.22370.21540.12120.069-0.1311-0.11820.2568-0.12660.1252-0.04910.03940.0899-0.01510.292-21.58926.905566.5939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1ALLA-4 - 144
2X-RAY DIFFRACTION2ALLB-4 - 144
3X-RAY DIFFRACTION3ALLC-4 - 143
4X-RAY DIFFRACTION4ALLD-4 - 145
5X-RAY DIFFRACTION5ALLE-4 - 144
6X-RAY DIFFRACTION6ALLF-4 - 145
7X-RAY DIFFRACTION7ALLG-4 - 144
8X-RAY DIFFRACTION8ALLH-4 - 146
9X-RAY DIFFRACTION9ALLI-4 - 143
10X-RAY DIFFRACTION10ALLJ-4 - 144
11X-RAY DIFFRACTION11ALLK-4 - 145
12X-RAY DIFFRACTION12ALLL-4 - 143

+
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