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- PDB-5gsw: Crystal structure of EV71 3C in complex with N69S 1.8k -

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Basic information

Entry
Database: PDB / ID: 5gsw
TitleCrystal structure of EV71 3C in complex with N69S 1.8k
Components3C protein
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / symbiont entry into host cell / virion attachment to host cell / proteolysis / RNA binding
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. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5GI / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsWang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81330036 China
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure of the Enterovirus 71 3C Protease in Complex with NK-1.8k and Indications for the Development of Antienterovirus Protease Inhibitor
Authors: Wang, Y. / Cao, L. / Zhai, Y. / Yin, Z. / Sun, Y. / Shang, L.
History
DepositionAug 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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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
C: 3C protein
D: 3C protein
E: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,03310
Polymers100,8115
Non-polymers2,2225
Water55831
1
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.501, 70.535, 94.923
Angle α, β, γ (deg.)90.00, 118.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3C protein


Mass: 20162.107 Da / Num. of mol.: 5 / Mutation: N69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: E7E815
#2: Chemical
ChemComp-5GI / ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide


Mass: 444.456 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C22H25FN4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M Tris-HCl, pH 7.7, 200 mM Sodium Citrate, 16% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 17983 / % possible obs: 96.8 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.36
Reflection shellResolution: 3.2→8.67 Å / Rmerge(I) obs: 0.581

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSY

3osy


Resolution: 3.19→48.62 Å / SU ML: 0.48 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.268 1831 10.18 %
Rwork0.189 --
obs0.197 17983 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.19→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6981 0 160 31 7172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127286
X-RAY DIFFRACTIONf_angle_d1.6229864
X-RAY DIFFRACTIONf_dihedral_angle_d18.4542639
X-RAY DIFFRACTIONf_chiral_restr0.0591135
X-RAY DIFFRACTIONf_plane_restr0.0061263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1901-3.27630.37981220.33481072X-RAY DIFFRACTION84
3.2763-3.37270.3781240.26561218X-RAY DIFFRACTION94
3.3727-3.48150.30431420.23571189X-RAY DIFFRACTION95
3.4815-3.60590.32221300.22291219X-RAY DIFFRACTION95
3.6059-3.75020.32971510.2051209X-RAY DIFFRACTION96
3.7502-3.92080.25431390.18571241X-RAY DIFFRACTION97
3.9208-4.12750.27931370.16631262X-RAY DIFFRACTION98
4.1275-4.38590.22421340.15291280X-RAY DIFFRACTION99
4.3859-4.72430.25081440.13981279X-RAY DIFFRACTION100
4.7243-5.19920.20731540.15481267X-RAY DIFFRACTION100
5.1992-5.95040.25831580.18511288X-RAY DIFFRACTION100
5.9504-7.49240.26311350.19791303X-RAY DIFFRACTION100
7.4924-48.62260.21941610.17131325X-RAY DIFFRACTION100
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)
11.6350.3668-0.16030.81460.11691.5339-0.0380.08940.0016-0.1351-0.05830.0240.23750.0353-00.2140.007-0.00460.05770.01740.099610.4428-1.218921.1246
21.56581.0251.08072.26140.7670.7586-0.0272-0.02840.01330.0134-0.01250.0783-0.0705-0.025300.10640.01390.01860.0969-0.00570.110618.300730.943933.7138
31.4938-0.3971-0.61651.1452-0.02681.55670.0383-0.0999-0.1847-0.120.0813-0.0482-0.04330.29100.1314-0.03570.00790.21080.00490.1804-22.135336.033915.7013
41.88090.1546-0.16591.32350.84020.97260.09590.29470.0043-0.206-0.0165-0.0564-0.0053-0.212300.1528-0.0008-0.01380.18740.06620.131639.043433.37795.5627
51.09820.6272-0.01271.59970.10590.7311-0.12630.01020.2309-0.14930.12720.02920.1324-0.3864-00.1801-0.0337-0.02310.3391-0.00370.2381-22.2358-1.698732.3772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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