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- PDB-7wyl: Structure of the EV71 3Cpro with 337 inhibitor -

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Basic information

Entry
Database: PDB / ID: 7wyl
TitleStructure of the EV71 3Cpro with 337 inhibitor
Components3C protein
KeywordsVIRAL PROTEIN / Structure of the EV71 3Cpro with 337 inhibitor
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-G7L / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsQin, B. / Hou, P. / Gao, X. / Cui, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772207 China
CitationJournal: Acta Pharm Sin B / Year: 2022
Title: Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 71 3C and SARS-CoV-2 main protease.
Authors: Qin, B. / Craven, G.B. / Hou, P. / Chesti, J. / Lu, X. / Child, E.S. / Morgan, R.M.L. / Niu, W. / Zhao, L. / Armstrong, A. / Mann, D.J. / Cui, S.
History
DepositionFeb 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 12, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C protein
B: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2933
Polymers41,0432
Non-polymers2501
Water7,026390
1
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7722
Polymers20,5221
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C protein


Theoretical massNumber of molelcules
Total (without water)20,5221
Polymers20,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.767, 70.497, 86.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3C protein / Protein 3B / Viral protein genome-linked


Mass: 20521.510 Da / Num. of mol.: 2 / Mutation: H133G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E7E815
#2: Chemical ChemComp-G7L / N-methyl-N-[[4-(trifluoromethyl)-1,3-thiazol-2-yl]methyl]prop-2-enamide


Mass: 250.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9F3N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 6%Tacsimate PH 7.0, 14% 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.28284 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28284 Å / Relative weight: 1
ReflectionResolution: 1.3→45.59 Å / Num. obs: 159196 / % possible obs: 92.5 % / Redundancy: 2.83 % / Biso Wilson estimate: 10.78 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.22
Reflection shellResolution: 1.3→3.89 Å / Num. unique obs: 23216 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r0f

3r0f


Resolution: 1.31→45.59 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 7809 4.97 %
Rwork0.2207 149185 -
obs0.2216 156994 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.83 Å2 / Biso mean: 18.0296 Å2 / Biso min: 3.98 Å2
Refinement stepCycle: final / Resolution: 1.31→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 27 390 3113
Biso mean--18.16 26.19 -
Num. residues----350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.31-1.320.23972580.2207443082
1.32-1.340.32532600.3051524097
1.34-1.350.32282900.3136527998
1.35-1.370.7391820.6506341163
1.37-1.390.61861920.6186358166
1.39-1.410.32472850.2624529299
1.41-1.430.26483110.2407527999
1.43-1.450.44922500.4137488190
1.45-1.470.46952520.4409473988
1.47-1.490.37862320.375483089
1.49-1.520.40252300.3557453984
1.52-1.550.45862090.4197421578
1.55-1.580.23022440.1996545299
1.58-1.610.21762530.19395413100
1.61-1.650.22532850.19455361100
1.65-1.680.2122200.18725458100
1.68-1.730.25382710.2065520897
1.73-1.770.21523000.1908536499
1.77-1.820.2043250.1903532999
1.82-1.880.20952900.2008523598
1.88-1.950.31231960.2843423778
1.95-2.030.19472810.1794528999
2.03-2.120.23682900.2342454285
2.12-2.230.20142990.1698535099
2.23-2.370.23032120.2047488689
2.37-2.560.19742690.17725364100
2.56-2.810.20082970.1891517496
2.81-3.220.19852710.1815368100
3.22-4.060.19472720.1697508494
4.06-45.590.17512830.1708535599

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