[English] 日本語
Yorodumi
- PDB-9rls: PARP10 catalytic domain in complex with OUL499 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rls
TitlePARP10 catalytic domain in complex with OUL499
ComponentsPoly [ADP-ribose] polymerase 10
KeywordsTRANSFERASE / Inhibitor / Complex / ADP-ribosyltransferase
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / : / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / negative regulation of NF-kappaB transcription factor activity / protein poly-ADP-ribosylation ...negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / : / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / negative regulation of NF-kappaB transcription factor activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / translesion synthesis / negative regulation of fibroblast proliferation / nucleotidyltransferase activity / transcription corepressor activity / chromatin organization / DNA-binding transcription factor binding / viral protein processing / negative regulation of gene expression / nucleolus / Golgi apparatus / nucleus / cytosol / cytoplasm
Similarity search - Function
PARP-10, RNA recognition motif 1 and 2 / PARP14, third RRM domain / : / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / Protein mono-ADP-ribosyltransferase PARP10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAlaviuhkola, J. / Lehtio, L.
Funding support Finland, 3items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Academy of Finland347026 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Optimization of 2,3-dihydrophthalazine-1,4-dione PARP inhibitor scaffold for nanomolar potency and specificity towards human PARP10.
Authors: Alaviuhkola, J. / Nizi, M.G. / Vagaggini, C. / Sarnari, C. / Lippok, B. / Maksimainen, M.M. / Bosetti, C. / Dhakar, S.S. / Manfroni, G. / Massari, S. / Dreassi, E. / Korn, P. / Tabarrini, O. / Lehtio, L.
History
DepositionJun 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 10
B: Poly [ADP-ribose] polymerase 10
C: Poly [ADP-ribose] polymerase 10
D: Poly [ADP-ribose] polymerase 10
E: Poly [ADP-ribose] polymerase 10
F: Poly [ADP-ribose] polymerase 10
G: Poly [ADP-ribose] polymerase 10
H: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,45016
Polymers173,0298
Non-polymers2,4228
Water97354
1
A: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9312
Polymers21,6291
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.590, 71.650, 131.460
Angle α, β, γ (deg.)102.572, 96.375, 90.006
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74A
84E
95A
105F
116A
126G
137A
147H
158B
168C
179B
189D
1910B
2010E
2111B
2211F
2312B
2412G
2513B
2613H
2714C
2814D
2915C
3015E
3116C
3216F
3317C
3417G
3518C
3618H
3719D
3819E
3920D
4020F
4121D
4221G
4322D
4422H
4523E
4623F
4724E
4824G
4925E
5025H
5126F
5226G
5327F
5427H
5528G
5628H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVALAA817 - 10071 - 191
221SERSERVALVALBB817 - 10071 - 191
332SERSERVALVALAA817 - 10071 - 191
442SERSERVALVALCC817 - 10071 - 191
553SERSERVALVALAA817 - 10071 - 191
663SERSERVALVALDD817 - 10071 - 191
774SERSERVALVALAA817 - 10071 - 191
884SERSERVALVALEE817 - 10071 - 191
995LEULEUHISHISAA820 - 10064 - 190
10105LEULEUHISHISFF820 - 10064 - 190
11116SERSERVALVALAA817 - 10071 - 191
12126SERSERVALVALGG817 - 10071 - 191
13137SERSERVALVALAA817 - 10071 - 191
14147SERSERVALVALHH817 - 10071 - 191
15158SERSERVALVALBB817 - 10071 - 191
16168SERSERVALVALCC817 - 10071 - 191
17179SERSERVALVALBB817 - 10071 - 191
18189SERSERVALVALDD817 - 10071 - 191
191910SERSERVALVALBB817 - 10071 - 191
202010SERSERVALVALEE817 - 10071 - 191
212111LEULEUHISHISBB820 - 10064 - 190
222211LEULEUHISHISFF820 - 10064 - 190
232312SERSERVALVALBB817 - 10071 - 191
242412SERSERVALVALGG817 - 10071 - 191
252513SERSERVALVALBB817 - 10071 - 191
262613SERSERVALVALHH817 - 10071 - 191
272714SERSERVALVALCC817 - 10071 - 191
282814SERSERVALVALDD817 - 10071 - 191
292915SERSERVALVALCC817 - 10071 - 191
303015SERSERVALVALEE817 - 10071 - 191
313116LEULEUHISHISCC820 - 10064 - 190
323216LEULEUHISHISFF820 - 10064 - 190
333317SERSERVALVALCC817 - 10071 - 191
343417SERSERVALVALGG817 - 10071 - 191
353518SERSERVALVALCC817 - 10071 - 191
363618SERSERVALVALHH817 - 10071 - 191
373719SERSERVALVALDD817 - 10071 - 191
383819SERSERVALVALEE817 - 10071 - 191
393920LEULEUHISHISDD820 - 10064 - 190
404020LEULEUHISHISFF820 - 10064 - 190
414121SERSERVALVALDD817 - 10071 - 191
424221SERSERVALVALGG817 - 10071 - 191
434322SERSERVALVALDD817 - 10071 - 191
444422SERSERVALVALHH817 - 10071 - 191
454523LEULEUHISHISEE820 - 10064 - 190
464623LEULEUHISHISFF820 - 10064 - 190
474724SERSERVALVALEE817 - 10071 - 191
484824SERSERVALVALGG817 - 10071 - 191
494925SERSERVALVALEE817 - 10071 - 191
505025SERSERVALVALHH817 - 10071 - 191
515126LEULEUHISHISFF820 - 10064 - 190
525226LEULEUHISHISGG820 - 10064 - 190
535327LEULEUHISHISFF820 - 10064 - 190
545427LEULEUHISHISHH820 - 10064 - 190
555528SERSERVALVALGG817 - 10071 - 191
565628SERSERVALVALHH817 - 10071 - 191

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

-
Components

#1: Protein
Poly [ADP-ribose] polymerase 10 / PARP-10 / ADP-ribosyltransferase diphtheria toxin-like 10 / ARTD10


Mass: 21628.586 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP10 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q53GL7, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-A1JHC / 6-[(3-chlorophenyl)methoxy]-2,3-dihydrophthalazine-1,4-dione


Mass: 302.712 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 10% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 40627 / % possible obs: 90.9 % / Redundancy: 1.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.075 / Net I/σ(I): 10.01
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.335 / Num. unique obs: 1999 / CC1/2: 0.739 / Rrim(I) all: 0.473 / % possible all: 60.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48.321 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 16.564 / SU ML: 0.324 / Cross valid method: FREE R-VALUE / ESU R Free: 0.43
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2645 2032 5.002 %
Rwork0.214 38595 -
all0.217 --
obs-40627 90.911 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.846 Å2
Baniso -1Baniso -2Baniso -3
1--1.057 Å20.504 Å20.343 Å2
2--0.156 Å2-1.006 Å2
3---1.131 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11992 0 168 54 12214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312458
X-RAY DIFFRACTIONr_bond_other_d0.0010.01411575
X-RAY DIFFRACTIONr_angle_refined_deg1.691.65616922
X-RAY DIFFRACTIONr_angle_other_deg1.211.57726383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67551493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.98319.155805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.561151914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.05715168
X-RAY DIFFRACTIONr_chiral_restr0.0660.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023286
X-RAY DIFFRACTIONr_nbd_refined0.2060.22008
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.210742
X-RAY DIFFRACTIONr_nbtor_refined0.1660.25760
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.26849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.232
X-RAY DIFFRACTIONr_nbd_other0.2260.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.213
X-RAY DIFFRACTIONr_mcbond_it5.4045.0946014
X-RAY DIFFRACTIONr_mcbond_other5.3975.0936013
X-RAY DIFFRACTIONr_mcangle_it7.9087.6257490
X-RAY DIFFRACTIONr_mcangle_other7.917.6267491
X-RAY DIFFRACTIONr_scbond_it5.6515.5276444
X-RAY DIFFRACTIONr_scbond_other5.655.5276445
X-RAY DIFFRACTIONr_scangle_it8.4718.1189431
X-RAY DIFFRACTIONr_scangle_other8.478.1189432
X-RAY DIFFRACTIONr_lrange_it11.04756.24412778
X-RAY DIFFRACTIONr_lrange_other11.04756.24212779
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.055918
X-RAY DIFFRACTIONr_ncsr_local_group_20.040.055940
X-RAY DIFFRACTIONr_ncsr_local_group_30.0550.055935
X-RAY DIFFRACTIONr_ncsr_local_group_40.0490.055924
X-RAY DIFFRACTIONr_ncsr_local_group_50.0530.055833
X-RAY DIFFRACTIONr_ncsr_local_group_60.0570.055903
X-RAY DIFFRACTIONr_ncsr_local_group_70.0390.055972
X-RAY DIFFRACTIONr_ncsr_local_group_80.0540.055898
X-RAY DIFFRACTIONr_ncsr_local_group_90.0560.055943
X-RAY DIFFRACTIONr_ncsr_local_group_100.0520.055864
X-RAY DIFFRACTIONr_ncsr_local_group_110.0540.055809
X-RAY DIFFRACTIONr_ncsr_local_group_120.0510.055934
X-RAY DIFFRACTIONr_ncsr_local_group_130.0490.055910
X-RAY DIFFRACTIONr_ncsr_local_group_140.0480.055959
X-RAY DIFFRACTIONr_ncsr_local_group_150.0440.055938
X-RAY DIFFRACTIONr_ncsr_local_group_160.0460.055837
X-RAY DIFFRACTIONr_ncsr_local_group_170.0580.055891
X-RAY DIFFRACTIONr_ncsr_local_group_180.0370.055958
X-RAY DIFFRACTIONr_ncsr_local_group_190.0470.055935
X-RAY DIFFRACTIONr_ncsr_local_group_200.0580.055832
X-RAY DIFFRACTIONr_ncsr_local_group_210.0660.055886
X-RAY DIFFRACTIONr_ncsr_local_group_220.0460.055954
X-RAY DIFFRACTIONr_ncsr_local_group_230.0480.055807
X-RAY DIFFRACTIONr_ncsr_local_group_240.0530.055872
X-RAY DIFFRACTIONr_ncsr_local_group_250.0350.055946
X-RAY DIFFRACTIONr_ncsr_local_group_260.0460.055854
X-RAY DIFFRACTIONr_ncsr_local_group_270.0450.055865
X-RAY DIFFRACTIONr_ncsr_local_group_280.0510.055907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.052790.0501
12BX-RAY DIFFRACTIONLocal ncs0.052790.0501
23AX-RAY DIFFRACTIONLocal ncs0.039860.0501
24CX-RAY DIFFRACTIONLocal ncs0.039860.0501
35AX-RAY DIFFRACTIONLocal ncs0.054930.0501
36DX-RAY DIFFRACTIONLocal ncs0.054930.0501
47AX-RAY DIFFRACTIONLocal ncs0.048980.0501
48EX-RAY DIFFRACTIONLocal ncs0.048980.0501
59AX-RAY DIFFRACTIONLocal ncs0.053190.0501
510FX-RAY DIFFRACTIONLocal ncs0.053190.0501
611AX-RAY DIFFRACTIONLocal ncs0.056510.0501
612GX-RAY DIFFRACTIONLocal ncs0.056510.0501
713AX-RAY DIFFRACTIONLocal ncs0.039330.0501
714HX-RAY DIFFRACTIONLocal ncs0.039330.0501
815BX-RAY DIFFRACTIONLocal ncs0.054360.0501
816CX-RAY DIFFRACTIONLocal ncs0.054360.0501
917BX-RAY DIFFRACTIONLocal ncs0.055980.05011
918DX-RAY DIFFRACTIONLocal ncs0.055980.05011
1019BX-RAY DIFFRACTIONLocal ncs0.051710.0501
1020EX-RAY DIFFRACTIONLocal ncs0.051710.0501
1121BX-RAY DIFFRACTIONLocal ncs0.054280.0501
1122FX-RAY DIFFRACTIONLocal ncs0.054280.0501
1223BX-RAY DIFFRACTIONLocal ncs0.051080.0501
1224GX-RAY DIFFRACTIONLocal ncs0.051080.0501
1325BX-RAY DIFFRACTIONLocal ncs0.048890.0501
1326HX-RAY DIFFRACTIONLocal ncs0.048890.0501
1427CX-RAY DIFFRACTIONLocal ncs0.047550.05011
1428DX-RAY DIFFRACTIONLocal ncs0.047550.05011
1529CX-RAY DIFFRACTIONLocal ncs0.043860.05011
1530EX-RAY DIFFRACTIONLocal ncs0.043860.05011
1631CX-RAY DIFFRACTIONLocal ncs0.046330.05011
1632FX-RAY DIFFRACTIONLocal ncs0.046330.05011
1733CX-RAY DIFFRACTIONLocal ncs0.057980.0501
1734GX-RAY DIFFRACTIONLocal ncs0.057980.0501
1835CX-RAY DIFFRACTIONLocal ncs0.037190.05011
1836HX-RAY DIFFRACTIONLocal ncs0.037190.05011
1937DX-RAY DIFFRACTIONLocal ncs0.047190.05011
1938EX-RAY DIFFRACTIONLocal ncs0.047190.05011
2039DX-RAY DIFFRACTIONLocal ncs0.057620.05011
2040FX-RAY DIFFRACTIONLocal ncs0.057620.05011
2141DX-RAY DIFFRACTIONLocal ncs0.065910.0501
2142GX-RAY DIFFRACTIONLocal ncs0.065910.0501
2243DX-RAY DIFFRACTIONLocal ncs0.046350.05011
2244HX-RAY DIFFRACTIONLocal ncs0.046350.05011
2345EX-RAY DIFFRACTIONLocal ncs0.048390.05011
2346FX-RAY DIFFRACTIONLocal ncs0.048390.05011
2447EX-RAY DIFFRACTIONLocal ncs0.052820.0501
2448GX-RAY DIFFRACTIONLocal ncs0.052820.0501
2549EX-RAY DIFFRACTIONLocal ncs0.034930.05011
2550HX-RAY DIFFRACTIONLocal ncs0.034930.05011
2651FX-RAY DIFFRACTIONLocal ncs0.046140.0501
2652GX-RAY DIFFRACTIONLocal ncs0.046140.0501
2753FX-RAY DIFFRACTIONLocal ncs0.0450.05011
2754HX-RAY DIFFRACTIONLocal ncs0.0450.05011
2855GX-RAY DIFFRACTIONLocal ncs0.051360.0501
2856HX-RAY DIFFRACTIONLocal ncs0.051360.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8220.3881000.3061899X-RAY DIFFRACTION60.6125
2.822-2.8990.3791200.3132282X-RAY DIFFRACTION74.1129
2.899-2.9830.311470.2682782X-RAY DIFFRACTION93.3992
2.983-3.0750.3211440.2322746X-RAY DIFFRACTION95.191
3.075-3.1750.2791410.2232677X-RAY DIFFRACTION96.1775
3.175-3.2870.3031390.2322640X-RAY DIFFRACTION96.6945
3.287-3.4110.3011300.2152466X-RAY DIFFRACTION95.2661
3.411-3.550.2521260.1982406X-RAY DIFFRACTION94.867
3.55-3.7080.2721220.2012300X-RAY DIFFRACTION95.6934
3.708-3.8880.2211140.2032183X-RAY DIFFRACTION94.6436
3.888-4.0990.2481100.1942081X-RAY DIFFRACTION94.5619
4.099-4.3470.2441040.2011971X-RAY DIFFRACTION94.3182
4.347-4.6470.235950.1811810X-RAY DIFFRACTION94.0276
4.647-5.0180.225910.181731X-RAY DIFFRACTION94.6002
5.018-5.4960.285830.221581X-RAY DIFFRACTION94.0644
5.496-6.1440.26760.2311447X-RAY DIFFRACTION95.8464
6.144-7.0920.278680.2181283X-RAY DIFFRACTION96.3623
7.092-8.6790.187550.1841051X-RAY DIFFRACTION94.2078
8.679-12.2450.216440.202823X-RAY DIFFRACTION93.9328
12.245-48.3210.418230.401436X-RAY DIFFRACTION92.5403

+
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