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- PDB-7wyo: Structure of the EV71 3Cpro with 338 inhibitor -

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Basic information

Entry
Database: PDB / ID: 7wyo
TitleStructure of the EV71 3Cpro with 338 inhibitor
Components3C protein
KeywordsVIRAL PROTEIN / EV71 3Cpro / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / cysteine-type endopeptidase activity / virion attachment to host cell / proteolysis / cytoplasm
Similarity search - Function
Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-G7F / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,2793
Polymers41,0432
Non-polymers2361
Water9,224512
1
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7582
Polymers20,5221
Non-polymers2361
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)59.721, 70.697, 85.394
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(DE3) (bacteria) / References: UniProt: E7E815
#2: Chemical ChemComp-G7F / N-methyl-N-(4,5,6,7-tetrahydro-1,3-benzothiazol-2-ylmethyl)prop-2-enamide


Mass: 236.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4% Tacsimate PH 7.0, 12% 3350

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.4→23.57 Å / Num. obs: 71310 / % possible obs: 99.7 % / Redundancy: 13.72 % / Biso Wilson estimate: 22.838 Å2 / CC1/2: 1 / Χ2: 0.86 / Net I/σ(I): 0.093
Reflection shellResolution: 1.4→1.49 Å / Num. unique obs: 11351 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0F

3r0f


Resolution: 1.402→23.124 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 3552 4.98 %
Rwork0.1838 67729 -
obs0.1845 71281 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.93 Å2 / Biso mean: 24.0248 Å2 / Biso min: 8.18 Å2
Refinement stepCycle: final / Resolution: 1.402→23.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 33 512 3268
Biso mean--22.36 33.52 -
Num. residues----352
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4021-1.42130.29181530.2527265399
1.4213-1.44160.2881250.25362693100
1.4416-1.46310.27031480.24732677100
1.4631-1.4860.34921420.26232655100
1.486-1.51030.26081450.22492690100
1.5103-1.53630.24451590.22362678100
1.5363-1.56430.22991440.21232672100
1.5643-1.59440.2321310.20092718100
1.5944-1.62690.23381530.20262651100
1.6269-1.66230.22721480.20332694100
1.6623-1.70090.23371540.2072682100
1.7009-1.74340.20961340.19292711100
1.7434-1.79060.21371470.19312684100
1.7906-1.84320.21731440.19762682100
1.8432-1.90270.21891370.209267898
1.9027-1.97070.21931320.2097267398
1.9707-2.04950.18261570.18432688100
2.0495-2.14270.20631480.17192726100
2.1427-2.25560.1981270.1889270199
2.2556-2.39680.19941410.1771270199
2.3968-2.58160.19171360.1772756100
2.5816-2.8410.18121290.1792758100
2.841-3.25120.19841420.16752764100
3.2512-4.09240.15921440.15922796100
4.0924-90.1581320.16792948100

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