[English] 日本語
Yorodumi
- PDB-6oyw: ASK1 kinase domain in complex with Compound 11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oyw
TitleASK1 kinase domain in complex with Compound 11
ComponentsMitogen-activated protein kinase kinase kinase 5
KeywordsTRANSFERASE / ASK1 MAP3K5
Function / homology
Function and homology information


cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of cardiac muscle cell apoptotic process / p38MAPK cascade / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / MAP kinase kinase kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of protein kinase activity / positive regulation of myoblast differentiation / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / apoptotic signaling pathway / positive regulation of JNK cascade / cellular response to hydrogen peroxide / MAPK cascade / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / neuron apoptotic process / Oxidative Stress Induced Senescence / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / Transferase(Phosphotransferase) domain 1 ...MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NKJ / Mitogen-activated protein kinase kinase kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsMarcotte, D.J.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Rational Design and Optimization of a Novel Class of Macrocyclic Apoptosis Signal-Regulating Kinase 1 Inhibitors.
Authors: Himmelbauer, M.K. / Xin, Z. / Jones, J.H. / Enyedy, I. / King, K. / Marcotte, D.J. / Murugan, P. / Santoro, J.C. / Hesson, T. / Spilker, K. / Johnson, J.L. / Luzzio, M.J. / Gilfillan, R. / de Turiso, F.G.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 5
B: Mitogen-activated protein kinase kinase kinase 5
C: Mitogen-activated protein kinase kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6819
Polymers132,2594
Non-polymers1,4225
Water4,540252
1
C: Mitogen-activated protein kinase kinase kinase 5
hetero molecules

A: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8525
Polymers66,1292
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area1980 Å2
ΔGint-13 kcal/mol
Surface area22160 Å2
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase 5
hetero molecules

D: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8284
Polymers66,1292
Non-polymers6992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_644-x+1,y-1/2,-z-1/21
Buried area1770 Å2
ΔGint-8 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.987, 130.415, 137.480
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
11(chain A and (resid 671 or (resid 672 and (name...
21(chain B and (resid 671 or (resid 672 and (name...
31(chain C and (resid 671 through 712 or (resid 713...
41(chain D and (resid 671 through 679 or (resid 680...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and (resid 671 or (resid 672 and (name...AA67114
12GLUGLUGLUGLU(chain A and (resid 671 or (resid 672 and (name...AA67215
13LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
14LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
15LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
16LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
21LEULEULEULEU(chain B and (resid 671 or (resid 672 and (name...BB67114
22GLUGLUGLUGLU(chain B and (resid 671 or (resid 672 and (name...BB67215
23LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
24LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
25LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
26LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
31LEULEUPROPRO(chain C and (resid 671 through 712 or (resid 713...CC671 - 71214 - 55
32GLUGLUGLNGLN(chain C and (resid 671 through 712 or (resid 713...CC713 - 72056 - 63
33LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
34LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
35LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
36LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
41LEULEUGLUGLU(chain D and (resid 671 through 679 or (resid 680...DD671 - 67914 - 22
42ASNASNASNASN(chain D and (resid 671 through 679 or (resid 680...DD68023
43LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282
44LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282
45LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282
46LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282

-
Components

#1: Protein
Mitogen-activated protein kinase kinase kinase 5 / Apoptosis signal-regulating kinase 1 / ASK-1 / MAPK/ERK kinase kinase 5 / MEKK 5


Mass: 33064.676 Da / Num. of mol.: 4 / Mutation: T838E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K5, ASK1, MAPKKK5, MEKK5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#2: Chemical
ChemComp-NKJ / (19S)-19-methyl-16,17,18,19-tetrahydro-8,4-(azeno)[1,2,4]triazolo[4,3-f][1,6,13]benzoxadiazacyclohexadecin-10(9H)-one


Mass: 349.386 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19N5O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BisTRIS pH 5.5, 0.2M MgCl2, 10mM Na cholate and 12% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 42652 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.187 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.747 / Num. unique obs: 6142 / CC1/2: 0.677 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BF2
Resolution: 2.603→29.962 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 2087 4.9 %
Rwork0.2078 40489 -
obs0.21 42576 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.33 Å2 / Biso mean: 41.6527 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 2.603→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8008 0 105 252 8365
Biso mean--26.63 36.49 -
Num. residues----1037
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2984X-RAY DIFFRACTION7.52TORSIONAL
12B2984X-RAY DIFFRACTION7.52TORSIONAL
13C2984X-RAY DIFFRACTION7.52TORSIONAL
14D2984X-RAY DIFFRACTION7.52TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6028-2.66330.35351440.300226502794100
2.6633-2.72990.33191410.266426492790100
2.7299-2.80360.30711490.252626582807100
2.8036-2.8860.28151590.249226422801100
2.886-2.97910.27931220.250726582780100
2.9791-3.08550.29591260.240327022828100
3.0855-3.20890.27951440.240826842828100
3.2089-3.35480.29091590.23326522811100
3.3548-3.53140.27241240.217826892813100
3.5314-3.75220.27561210.194627142835100
3.7522-4.04130.23241120.178427312843100
4.0413-4.44680.18941270.163327312858100
4.4468-5.08760.18081380.154727392877100
5.0876-6.39950.26141690.208727292898100
6.3995-29.96410.23221520.1972861301399
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)
13.29952.4293-1.17934.6621-1.78924.05240.5645-0.6415-0.27720.8454-0.4613-0.5145-0.22770.7571-0.13760.4435-0.114-0.130.3448-0.02310.447641.016.585432.9625
21.7137-0.143-0.61162.39160.35733.0303-0.0193-0.0060.01880.1364-0.0043-0.01050.1032-0.18980.03430.2001-0.0364-0.01990.20010.00480.304333.98027.690318.5311
34.94482.2488-1.36775.9888-0.43944.5130.09330.25460.5975-0.2044-0.0560.4451-0.9283-0.5682-0.0680.44930.0832-0.04950.3088-0.09260.365830.961217.976613.1018
42.6346-0.6165-1.81724.2586-1.05633.75810.05230.2256-0.1464-0.3548-0.03440.07550.0365-0.29180.01780.2911-0.0374-0.06730.2846-0.01410.193436.699111.1021-1.0523
58.46351.9973-5.49644.7488-1.33023.6358-0.51320.5377-0.6928-0.7752-0.05940.37210.4668-0.5210.48810.37370.1322-0.0560.5197-0.09180.357226.129912.8505-50.2907
63.458-0.603-0.80094.90652.62894.94030.06180.09980.0313-0.3964-0.47810.24-0.6907-0.06510.42210.32610.06080.00190.2470.00240.239332.356520.6909-45.8383
72.6987-1.64191.41994.2137-1.47164.16720.05420.23450.0689-0.10580.08340.11140.00140.0423-0.10730.2530.02320.07950.2498-0.04550.235540.683218.554-41.0597
81.1858-0.6097-0.1512.54810.75636.3479-0.0198-0.06930.18710.170.1838-0.162-0.30940.5105-0.13330.20670.0112-0.01430.3243-0.04260.286647.884721.2356-25.2051
97.6947-2.5652-3.91962.74952.44433.9392-0.5413-0.2393-0.52280.27930.342-0.81420.62511.7899-0.01670.31190.23920.07130.936-0.23980.331461.492314.5446-26.5787
100.52730.47241.08161.48941.35322.3645-0.10180.08860.1177-0.2867-0.23630.626-0.2579-0.2199-0.19020.70950.1188-0.58020.3771-0.28871.0541-8.67618.6586-53.5928
112.4205-1.9144-0.12294.43783.05213.9267-0.3860.0510.1916-1.0954-0.16641.1411-0.7109-0.1340.33230.3241-0.0138-0.15720.22630.00650.611-1.916420.1377-49.3859
122.5807-0.8276-1.77591.7276-0.88252.6755-0.07940.06580.8111-0.62810.01470.3491-0.9098-0.646-0.11580.71110.1321-0.23380.24480.01960.8785-0.891527.2987-49.3114
133.6956-1.4960.58293.6527-1.64124.0053-0.340.1371.0708-0.61190.00270.2985-0.62180.22210.17790.5896-0.0139-0.13960.23810.03850.58927.385425.4424-49.1026
142.43711.12570.33344.09051.07713.11440.0633-0.16430.01480.2916-0.13260.47630.324-0.03960.01230.24670.00880.05130.1803-0.02670.30968.343715.4638-33.504
154.0862-1.212-2.4917.8649-1.42518.44230.41790.41420.23730.1820.17610.459-1.0235-0.1112-0.59040.32710.0463-0.07820.2956-0.00610.3869.749132.7154-30.9915
161.7245-0.47820.39194.35790.8263.3232-0.0659-0.51930.38111.1036-0.06680.8697-0.1126-0.26360.06380.4893-0.02370.13580.307-0.07470.47797.159926.9766-21.2755
176.71160.1753-1.866.2559-2.7896.8621-0.0604-0.27480.03531.42090.2258-0.45290.47440.034-0.06770.48210.0073-0.0730.2671-0.0110.247316.648617.463-19.2308
184.20453.96724.41298.5438-0.18758.5849-0.42040.4568-0.1556-1.65970.063-0.84750.06170.60910.34940.91020.04950.24630.4917-0.0860.532438.165856.0263-39.1434
195.044-1.16491.49054.4918-0.53683.20650.01610.408-0.2678-0.9813-0.0345-0.5360.16570.64220.06370.4271-0.0710.06840.2788-0.02660.281633.323652.9108-32.0838
202.12531.38341.62534.6851.77454.7687-0.00330.1201-0.1944-0.47550.0647-0.0001-0.0140.0922-0.06330.2511-0.0360.02070.23880.03960.311930.693754.5388-23.072
211.21480.81650.97823.2830.51622.29540.1114-0.2448-0.09880.4009-0.02790.412-0.0329-0.0805-0.07820.1971-0.04010.0630.28580.06410.308430.047159.4672-12.2034
226.56076.25-3.01377.3292-0.94085.0281-0.4905-0.0735-0.47780.0046-0.058-0.03591.2205-0.15740.43020.5037-0.05510.05060.2277-0.04070.443928.057444.6793-14.0133
236.4185-0.09690.37316.4636-0.52064.52710.1296-0.3306-0.4510.1527-0.1258-0.17960.74310.43970.07750.3310.01160.01160.28770.05150.260334.654448.7241-4.5351
245.4602-0.031-0.57282.1122-1.89727.9352-0.03230.1341-0.76640.42790.0296-0.92270.83331.07360.04970.45620.1133-0.1180.51540.03830.819945.548344.7528-3.2588
255.2215-1.42240.41417.24551.8145.9893-0.0836-0.3806-0.18151.57150.2486-0.62320.38090.0482-0.0990.5903-0.1081-0.08820.47050.08460.286638.996857.67694.0806
265.9204-0.04671.17474.171-1.07095.64180.0685-0.7078-0.03410.819-0.00530.98320.3293-0.629-0.01810.427-0.02160.18830.4830.03160.359727.138456.69042.4168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 671 through 703 )A671 - 703
2X-RAY DIFFRACTION2chain 'A' and (resid 704 through 817 )A704 - 817
3X-RAY DIFFRACTION3chain 'A' and (resid 818 through 840 )A818 - 840
4X-RAY DIFFRACTION4chain 'A' and (resid 841 through 939 )A841 - 939
5X-RAY DIFFRACTION5chain 'B' and (resid 671 through 684 )B671 - 684
6X-RAY DIFFRACTION6chain 'B' and (resid 685 through 718 )B685 - 718
7X-RAY DIFFRACTION7chain 'B' and (resid 719 through 776 )B719 - 776
8X-RAY DIFFRACTION8chain 'B' and (resid 777 through 928 )B777 - 928
9X-RAY DIFFRACTION9chain 'B' and (resid 929 through 940 )B929 - 940
10X-RAY DIFFRACTION10chain 'C' and (resid 671 through 684 )C671 - 684
11X-RAY DIFFRACTION11chain 'C' and (resid 685 through 703 )C685 - 703
12X-RAY DIFFRACTION12chain 'C' and (resid 704 through 719 )C704 - 719
13X-RAY DIFFRACTION13chain 'C' and (resid 720 through 755 )C720 - 755
14X-RAY DIFFRACTION14chain 'C' and (resid 756 through 825 )C756 - 825
15X-RAY DIFFRACTION15chain 'C' and (resid 826 through 847 )C826 - 847
16X-RAY DIFFRACTION16chain 'C' and (resid 848 through 897 )C848 - 897
17X-RAY DIFFRACTION17chain 'C' and (resid 898 through 939 )C898 - 939
18X-RAY DIFFRACTION18chain 'D' and (resid 671 through 684 )D671 - 684
19X-RAY DIFFRACTION19chain 'D' and (resid 685 through 715 )D685 - 715
20X-RAY DIFFRACTION20chain 'D' and (resid 716 through 776 )D716 - 776
21X-RAY DIFFRACTION21chain 'D' and (resid 777 through 820 )D777 - 820
22X-RAY DIFFRACTION22chain 'D' and (resid 821 through 842 )D821 - 842
23X-RAY DIFFRACTION23chain 'D' and (resid 843 through 876 )D843 - 876
24X-RAY DIFFRACTION24chain 'D' and (resid 877 through 897 )D877 - 897
25X-RAY DIFFRACTION25chain 'D' and (resid 898 through 919 )D898 - 919
26X-RAY DIFFRACTION26chain 'D' and (resid 920 through 939 )D920 - 939

+
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