[English] 日本語
Yorodumi
- PDB-6mc1: Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mc1
TitleStructure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-(methylthio)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor
ComponentsDual specificity protein phosphatase 10
KeywordsHydrolase/Hydrolase Inhibitor / phosphatase / protein-tyrosine phosphatase / dual specificity phosphatase / phosphatase-inhibitor complex / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / Signaling by MAPK mutants / negative regulation of oligodendrocyte differentiation / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / negative regulation of JNK cascade / JUN kinase binding / positive regulation of regulatory T cell differentiation / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
ACETATE ION / Chem-CJA / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGannam, Z.T.K. / Anderson, K.S. / Bennett, A.M. / Lolis, E.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)5T32AI055403-12 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR066003 United States
CitationJournal: Sci.Signal. / Year: 2020
Title: An allosteric site on MKP5 reveals a strategy for small-molecule inhibition.
Authors: Gannam, Z.T.K. / Min, K. / Shillingford, S.R. / Zhang, L. / Herrington, J. / Abriola, L. / Gareiss, P.C. / Pantouris, G. / Tzouvelekis, A. / Kaminski, N. / Zhang, X. / Yu, J. / Jamali, H. / ...Authors: Gannam, Z.T.K. / Min, K. / Shillingford, S.R. / Zhang, L. / Herrington, J. / Abriola, L. / Gareiss, P.C. / Pantouris, G. / Tzouvelekis, A. / Kaminski, N. / Zhang, X. / Yu, J. / Jamali, H. / Ellman, J.A. / Lolis, E. / Anderson, K.S. / Bennett, A.M.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10
C: Dual specificity protein phosphatase 10
D: Dual specificity protein phosphatase 10
E: Dual specificity protein phosphatase 10
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,71718
Polymers104,7006
Non-polymers3,01812
Water0
1
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8152
Polymers17,4501
Non-polymers3651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0284
Polymers17,4501
Non-polymers5783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9693
Polymers17,4501
Non-polymers5192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9693
Polymers17,4501
Non-polymers5192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9693
Polymers17,4501
Non-polymers5192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9693
Polymers17,4501
Non-polymers5192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.110, 129.390, 83.310
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 320 through 333 or (resid 334...
21(chain B and ((resid 320 through 321 and (name N...
31(chain C and ((resid 320 through 321 and (name N...
41(chain D and (resid 320 through 333 or (resid 334...
51(chain E and ((resid 320 through 321 and (name N...
61(chain F and ((resid 320 through 321 and (name N...

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
11ALAALAASNASN(chain A and (resid 320 through 333 or (resid 334...AA320 - 3335 - 18
12GLUGLUGLUGLU(chain A and (resid 320 through 333 or (resid 334...AA33419
13ALAALACJACJA(chain A and (resid 320 through 333 or (resid 334...AA - G320 - 5005
14ALAALACJACJA(chain A and (resid 320 through 333 or (resid 334...AA - G320 - 5005
15ALAALACJACJA(chain A and (resid 320 through 333 or (resid 334...AA - G320 - 5005
16ALAALACJACJA(chain A and (resid 320 through 333 or (resid 334...AA - G320 - 5005
21ALAALAGLUGLU(chain B and ((resid 320 through 321 and (name N...BB320 - 3215 - 6
22ALAALAACTACT(chain B and ((resid 320 through 321 and (name N...BB - J320 - 5025
23ALAALAACTACT(chain B and ((resid 320 through 321 and (name N...BB - J320 - 5025
24ALAALAACTACT(chain B and ((resid 320 through 321 and (name N...BB - J320 - 5025
25ALAALAACTACT(chain B and ((resid 320 through 321 and (name N...BB - J320 - 5025
31ALAALAGLUGLU(chain C and ((resid 320 through 321 and (name N...CC320 - 3215 - 6
32METMETDTTDTT(chain C and ((resid 320 through 321 and (name N...CC - L319 - 5014
33METMETDTTDTT(chain C and ((resid 320 through 321 and (name N...CC - L319 - 5014
34METMETDTTDTT(chain C and ((resid 320 through 321 and (name N...CC - L319 - 5014
35METMETDTTDTT(chain C and ((resid 320 through 321 and (name N...CC - L319 - 5014
41ALAALAASNASN(chain D and (resid 320 through 333 or (resid 334...DD320 - 3335 - 18
42GLUGLUGLUGLU(chain D and (resid 320 through 333 or (resid 334...DD33419
43ALAALADTTDTT(chain D and (resid 320 through 333 or (resid 334...DD - N320 - 5015
44ALAALADTTDTT(chain D and (resid 320 through 333 or (resid 334...DD - N320 - 5015
45ALAALADTTDTT(chain D and (resid 320 through 333 or (resid 334...DD - N320 - 5015
46ALAALADTTDTT(chain D and (resid 320 through 333 or (resid 334...DD - N320 - 5015
51ALAALAGLUGLU(chain E and ((resid 320 through 321 and (name N...EE320 - 3215 - 6
52ALAALADTTDTT(chain E and ((resid 320 through 321 and (name N...EE - P320 - 5015
53ALAALADTTDTT(chain E and ((resid 320 through 321 and (name N...EE - P320 - 5015
54ALAALADTTDTT(chain E and ((resid 320 through 321 and (name N...EE - P320 - 5015
55ALAALADTTDTT(chain E and ((resid 320 through 321 and (name N...EE - P320 - 5015
61ALAALAGLUGLU(chain F and ((resid 320 through 321 and (name N...FF320 - 3215 - 6
62ALAALADTTDTT(chain F and ((resid 320 through 321 and (name N...FF - R320 - 5015
63ALAALADTTDTT(chain F and ((resid 320 through 321 and (name N...FF - R320 - 5015
64ALAALADTTDTT(chain F and ((resid 320 through 321 and (name N...FF - R320 - 5015
65ALAALADTTDTT(chain F and ((resid 320 through 321 and (name N...FF - R320 - 5015

-
Components

#1: Protein
Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MKP-5


Mass: 17449.961 Da / Num. of mol.: 6 / Fragment: UNP residues 320-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-CJA / 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one


Mass: 364.549 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H20N2OS3
#3: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.84 % / Description: thin plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 200 mM ammonium acetate, 100 mM HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→48.707 Å / Num. obs: 38356 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.707 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.201 / Rrim(I) all: 0.235 / Χ2: 1.019 / Net I/σ(I): 7.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.773.7451.2841.4928310.5231.49999.8
2.77-2.853.7481.1711.6527410.5461.36899.6
2.85-2.933.7320.971226750.6471.13599.5
2.93-3.023.7250.7972.4826180.7310.93199.6
3.02-3.123.7520.695324960.7150.81299.5
3.12-3.233.7820.5454.2724580.8020.63799.6
3.23-3.353.7990.4255.623570.8570.49699.7
3.35-3.493.7740.3616.522850.8770.42299.8
3.49-3.643.7970.2697.8521590.9250.31599.9
3.64-3.823.7250.2049.4120810.9520.23999.9
3.82-4.023.6940.15411.1119980.9720.18199.7
4.02-4.273.6570.1212.6518620.9820.14199.7
4.27-4.563.5830.09614.0817670.9890.11399.5
4.56-4.933.5330.08514.9116450.990.199.7
4.93-5.43.630.08514.4715120.9910.10199.6
5.4-6.043.6140.09113.5413850.9890.10799.9
6.04-6.973.70.08813.9812160.990.10399.8
6.97-8.543.6090.05817.4810280.9960.06899.6
8.54-12.073.5620.03824.027990.9970.04599.9
12.07-48.7073.3840.03823.254430.9980.04598

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zzw

1zzw


Resolution: 2.7→48.707 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2002 5.22 %Random selection
Rwork0.188 ---
obs0.1901 38346 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.2 Å2 / Biso mean: 50.2663 Å2 / Biso min: 17.43 Å2
Refinement stepCycle: final / Resolution: 2.7→48.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 182 0 7292
Biso mean--66.14 --
Num. residues----881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057456
X-RAY DIFFRACTIONf_angle_d0.86310087
X-RAY DIFFRACTIONf_chiral_restr0.0521089
X-RAY DIFFRACTIONf_plane_restr0.0061296
X-RAY DIFFRACTIONf_dihedral_angle_d11.0884431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4263X-RAY DIFFRACTION7.364TORSIONAL
12B4263X-RAY DIFFRACTION7.364TORSIONAL
13C4263X-RAY DIFFRACTION7.364TORSIONAL
14D4263X-RAY DIFFRACTION7.364TORSIONAL
15E4263X-RAY DIFFRACTION7.364TORSIONAL
16F4263X-RAY DIFFRACTION7.364TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.76750.37441470.329325852732100
2.7675-2.84230.35381430.323225712714100
2.8423-2.92590.34731380.30312575271399
2.9259-3.02040.3541420.305925992741100
3.0204-3.12830.35991370.29072570270799
3.1283-3.25350.26251430.232325862729100
3.2535-3.40160.2911430.20626002743100
3.4016-3.58080.23241420.196326022744100
3.5808-3.80510.22031410.172525862727100
3.8051-4.09880.20041430.147726072750100
4.0988-4.5110.17681460.131125922738100
4.511-5.16310.12891400.127526212761100
5.1631-6.50250.18771490.159526052754100
6.5025-48.71520.18441480.148826452793100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2062-3.9619-0.76378.18642.92143.0006-0.1875-0.1812-0.41590.12020.4964-0.4491-0.34290.4001-0.32260.4388-0.0442-0.03510.4317-0.03830.363682.7056-94.680714.1384
23.87380.7144-2.37863.00712.05795.30360.2663-0.6490.20120.2947-0.1259-0.3332-0.26330.291-0.42840.46850.0078-0.0410.31270.02990.307187.4224-101.572814.5096
32.00670.35681.68464.9797-2.2683.47330.215-1.3082-0.39350.136-0.64960.1889-0.0816-0.05220.04340.4640.0321-0.03070.2701-0.06660.312688.9612-108.648514.9824
44.09630.042.62314.365-1.41228.17280.0672-0.0824-0.1704-0.07740.0690.31470.2982-0.2074-0.19860.2685-0.0397-0.00210.2682-0.01650.34876.1818-105.73784.4017
53.2615-1.59351.95583.7806-0.9325.11730.0747-0.08380.36450.33460.12660.1314-0.4016-0.6756-0.20770.38050.00490.05580.3421-0.00110.2973.9698-94.62216.9086
64.85726.4629-5.0339.6913-6.69025.2487-0.27460.96530.0773-0.44830.56421.03620.0607-0.9507-0.16740.4124-0.0793-0.00330.4321-0.01080.397266.3655-99.7166-3.5158
74.37082.6332-2.17233.5059-3.43893.3539-0.38210.3540.0025-0.6340.35640.29770.4569-0.39550.13940.3181-0.0113-0.01920.44630.01760.570458.0815-78.2142-25.7732
84.872.91913.63063.3209-0.50627.3040.3530.15630.26660.051-0.05910.3068-0.0776-0.15-0.33840.34840.0617-0.01580.268-0.03790.552260.2788-70.7047-16.9939
90.9385-0.44351.43576.4449-2.62348.2059-0.0738-0.1558-0.0034-0.0462-0.00910.32720.4801-0.24280.00150.23540.03390.0110.3571-0.0070.481860.3197-83.461-13.305
104.8659-0.3386-4.77695.04090.76694.78080.334-0.72591.1111.30370.2337-0.0074-0.18150.2046-0.38330.460.03480.08890.552-0.06450.592464.7015-78.4844-1.0347
115.2754-4.1191-5.87078.64736.08816.9550.75690.28450.17940.13610.3834-0.9258-0.28740.5532-1.47140.32630.0089-0.04410.5555-0.02840.3917107.344-91.2991-17.2459
122.55831.6549-2.29266.6454-4.26433.6255-0.00650.6146-0.1983-0.4299-0.078-0.65190.29670.1520.29710.29560.0598-0.05820.49690.02640.3573103.2971-91.4271-21.2972
133.59343.68741.5998.5061-1.9943.77861.50621.69070.603-1.2271-0.6652-0.24730.59521.3251-1.290.70590.1110.150.60670.04490.5815106.4796-100.9797-24.4063
144.48110.41031.88612.1622-3.30738.3840.01770.2255-0.416-0.4072-0.1456-0.1030.67340.13340.14690.3131-0.0376-0.03450.2276-0.06660.271996.3317-92.7366-25.6713
152.7245-0.7946-1.77687.29280.43144.1337-0.29220.0029-0.0677-0.67490.51440.08930.00610.2545-0.18890.2351-0.0194-0.12350.3289-0.00520.329391.5359-88.4361-25.3863
166.9432-4.19582.30092.5826-1.86344.4611-0.3665-0.832-0.9430.31010.96351.06870.8433-0.8245-0.44850.4574-0.02950.08540.38690.06220.351988.1795-92.8225-13.7686
173.96360.8618-0.05799.40872.49955.5127-0.2773-0.20840.0866-0.25110.0588-0.29410.03020.2625-0.19350.19660.0211-0.0010.2121-0.09030.375898.9187-90.1223-20.5292
183.7076-1.65221.35226.62174.32827.5752-0.1472-0.2132-0.23030.19430.16280.40121.03380.0809-0.09610.204-0.0123-0.00910.2515-0.020.287794.274-85.5723-11.4202
193.1655-0.07690.03897.6581.44796.130.0869-0.1423-0.00270.98610.2249-0.51450.17050.5604-0.31990.37880.0046-0.04520.2742-0.03210.3502101.6647-81.5299-8.727
206.51636.743-5.61788.1574-4.80056.14460.7735-0.24691.38651.37750.14210.6813-1.2056-0.4871-0.49080.37040.0338-0.01710.3995-0.05520.436388.2356-77.451-7.0495
212.03670.61670.70453.2096-0.03014.4583-0.15530.6965-0.3153-1.0456-0.0956-0.58150.00270.79250.28930.44890.0820.09980.61070.07460.590281.7452-59.4681-35.294
226.7451-3.41030.01786.3334-0.29545.6571-0.44370.0831-0.8242-0.10110.66140.45080.3283-0.3366-0.27420.26960.0241-0.0310.38720.17860.543575.4603-66.6042-28.0136
232.4054-2.172-0.96578.69580.11944.7499-0.0422-1.2968-0.39520.67820.3674-0.0373-0.3197-0.3909-0.38180.54160.10140.00920.42270.15120.373673.4409-52.5403-22.6618
244.8911-1.0473-0.47977.40380.30562.32430.0085-0.05570.3839-0.34080.0809-0.3857-0.2208-0.087-0.09470.33290.07840.02690.47060.15180.358875.6009-47.2305-32.9378
255.68081.7415.84796.7987-0.55168.3411-0.1292-0.83381.32860.69370.01210.7522-0.7783-1.1331-0.06080.48510.19520.10460.66830.06730.519468.4793-39.398-24.4263
268.0089-2.04275.7574.0003-1.00839.52390.25380.65030.4641-0.7965-0.2542-0.12740.03830.5787-0.10950.6322-0.06480.04980.40020.07040.32185.6716-86.0217-50.0652
275.6015-1.29925.24759.33420.95576.13940.27330.4547-0.5507-1.32510.6281-1.0003-1.66140.3157-0.89081.1023-0.2530.00730.86230.31170.849293.0371-77.9165-51.0625
287.7943-0.9791.88715.6421-3.29246.77190.0210.16860.3323-0.9172-0.036-0.16390.147-0.46860.06270.5088-0.0979-0.01190.3113-0.08150.250288.2539-84.3475-40.585
294.8059-0.3165-1.04874.3048-4.94566.2073-0.06850.65480.61990.0854-0.409-0.7113-0.23850.05360.32230.55580.0316-0.07120.26540.00240.446990.5912-78.6698-37.4554
302.8489-1.94432.77222.57970.61447.8703-0.0289-0.4494-0.4117-0.13610.0212-0.48610.22520.17290.19470.4824-0.09850.07980.3207-0.01280.378479.4553-97.5567-34.3585
316.59352.6815-1.47265.3083-4.71674.4097-0.1988-0.53831.22831.1216-0.2430.3676-1.2171-1.39130.14560.73740.126-0.07260.5951-0.18360.487374.3512-81.4191-38.619
325.39950.99391.57785.03131.01115.5871-0.25170.1620.212-0.38640.11520.4725-0.1857-0.3560.19580.40440.0188-0.01640.283-0.04220.286875.5849-90.8761-48.1235
334.2761-0.01973.89513.8517-2.98887.0939-0.4894-1.1266-0.51630.60570.29431.07930.0376-1.2948-0.22450.4229-0.03280.0030.6714-0.09850.443865.9522-96.3986-40.6524
349.24210.0718-0.48129.1508-7.56856.69290.07640.26130.30950.6904-0.19150.8336-0.3382-0.65230.16250.5328-0.04050.02230.354-0.13860.474490.8445-51.54541.8521
352.37892.8284-1.55513.9504-0.12537.01490.5096-0.10550.50270.3351-0.2210.6495-0.9198-0.0083-0.55770.4355-0.02690.0820.2636-0.06240.448595.9678-44.87972.8081
365.6381-0.9709-3.91894.32243.59056.38270.20230.00650.66910.1247-0.2598-0.4114-1.2597-0.078-0.36060.493-0.0380.04290.3329-0.03460.3729101.3964-40.89245.2574
377.6649-3.3606-2.45893.62813.36193.35530.02170.8329-0.1571-1.3661-0.1971-0.4178-0.28290.0640.080.581-0.0510.07510.3391-0.09130.4132107.9977-57.0745-8.0571
387.8811-5.4629-5.85384.80995.10125.56650.0289-1.1811-0.51722.07380.0984-1.05080.37440.7015-0.0890.8201-0.1531-0.11250.51370.02330.4728105.5259-56.34278.8349
394.13822.0227-0.21777.48571.28932.860.0424-0.1435-0.10150.1443-0.03520.42880.3694-0.31020.07240.3858-0.0223-0.00040.3-0.04130.300295.9259-61.54760.9917
403.49972.9534-4.51138.1539-3.08216.58440.2491-0.2271-0.75040.4158-0.6472-0.45431.02051.21860.61550.5567-0.0847-0.05430.4931-0.08080.4668106.6666-70.2725-0.4151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 320 through 339 )A320 - 339
2X-RAY DIFFRACTION2chain 'A' and (resid 340 through 362 )A340 - 362
3X-RAY DIFFRACTION3chain 'A' and (resid 363 through 372 )A363 - 372
4X-RAY DIFFRACTION4chain 'A' and (resid 373 through 400 )A373 - 400
5X-RAY DIFFRACTION5chain 'A' and (resid 401 through 448 )A401 - 448
6X-RAY DIFFRACTION6chain 'A' and (resid 449 through 466 )A449 - 466
7X-RAY DIFFRACTION7chain 'B' and (resid 320 through 362 )B320 - 362
8X-RAY DIFFRACTION8chain 'B' and (resid 363 through 400 )B363 - 400
9X-RAY DIFFRACTION9chain 'B' and (resid 401 through 448 )B401 - 448
10X-RAY DIFFRACTION10chain 'B' and (resid 449 through 467 )B449 - 467
11X-RAY DIFFRACTION11chain 'C' and (resid 319 through 326 )C319 - 326
12X-RAY DIFFRACTION12chain 'C' and (resid 327 through 339 )C327 - 339
13X-RAY DIFFRACTION13chain 'C' and (resid 340 through 345 )C340 - 345
14X-RAY DIFFRACTION14chain 'C' and (resid 346 through 362 )C346 - 362
15X-RAY DIFFRACTION15chain 'C' and (resid 363 through 383 )C363 - 383
16X-RAY DIFFRACTION16chain 'C' and (resid 384 through 400 )C384 - 400
17X-RAY DIFFRACTION17chain 'C' and (resid 401 through 412 )C401 - 412
18X-RAY DIFFRACTION18chain 'C' and (resid 413 through 426 )C413 - 426
19X-RAY DIFFRACTION19chain 'C' and (resid 427 through 448 )C427 - 448
20X-RAY DIFFRACTION20chain 'C' and (resid 449 through 466 )C449 - 466
21X-RAY DIFFRACTION21chain 'D' and (resid 320 through 353 )D320 - 353
22X-RAY DIFFRACTION22chain 'D' and (resid 354 through 372 )D354 - 372
23X-RAY DIFFRACTION23chain 'D' and (resid 373 through 400 )D373 - 400
24X-RAY DIFFRACTION24chain 'D' and (resid 401 through 448 )D401 - 448
25X-RAY DIFFRACTION25chain 'D' and (resid 449 through 465 )D449 - 465
26X-RAY DIFFRACTION26chain 'E' and (resid 320 through 339 )E320 - 339
27X-RAY DIFFRACTION27chain 'E' and (resid 340 through 345 )E340 - 345
28X-RAY DIFFRACTION28chain 'E' and (resid 346 through 362 )E346 - 362
29X-RAY DIFFRACTION29chain 'E' and (resid 363 through 372 )E363 - 372
30X-RAY DIFFRACTION30chain 'E' and (resid 373 through 383 )E373 - 383
31X-RAY DIFFRACTION31chain 'E' and (resid 384 through 400 )E384 - 400
32X-RAY DIFFRACTION32chain 'E' and (resid 401 through 448 )E401 - 448
33X-RAY DIFFRACTION33chain 'E' and (resid 449 through 464 )E449 - 464
34X-RAY DIFFRACTION34chain 'F' and (resid 320 through 339 )F320 - 339
35X-RAY DIFFRACTION35chain 'F' and (resid 340 through 362 )F340 - 362
36X-RAY DIFFRACTION36chain 'F' and (resid 363 through 372 )F363 - 372
37X-RAY DIFFRACTION37chain 'F' and (resid 373 through 383 )F373 - 383
38X-RAY DIFFRACTION38chain 'F' and (resid 384 through 400 )F384 - 400
39X-RAY DIFFRACTION39chain 'F' and (resid 401 through 448 )F401 - 448
40X-RAY DIFFRACTION40chain 'F' and (resid 449 through 466 )F449 - 466

+
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