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- PDB-5wq2: Crystal structure of 3C protease from a mild Human enterovirus 71... -

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Basic information

Entry
Database: PDB / ID: 5wq2
TitleCrystal structure of 3C protease from a mild Human enterovirus 71 in complex with rupintrivir
Components3C protein
KeywordsHYDROLASE / 3C / mutation / virus
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
Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLi, B. / Yuan, Z.
CitationJournal: To Be Published
Title: Crystal structure of 3C protease from a mild Human enterovirus 71 in complex with rupintrivir
Authors: Li, B. / Qin, L.
History
DepositionNov 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8854
Polymers20,0921
Non-polymers7933
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-25 kcal/mol
Surface area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.209, 64.781, 38.323
Angle α, β, γ (deg.)90.00, 113.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3C protein / 3C protease


Mass: 20092.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Escherichia coli (E. coli) / References: UniProt: E7E815
#2: Chemical ChemComp-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form


Mass: 600.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Comment: antivirus, protease inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 28% PEG 8000, Acetate PH4.5, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 32549 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 22.38

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→23.224 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14
RfactorNum. reflection% reflection
Rfree0.1991 2017 6.2 %
Rwork0.1743 --
obs0.1758 32549 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.39→23.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 53 236 1698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081563
X-RAY DIFFRACTIONf_angle_d1.1912130
X-RAY DIFFRACTIONf_dihedral_angle_d14.254573
X-RAY DIFFRACTIONf_chiral_restr0.087242
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.42470.26731460.22652136X-RAY DIFFRACTION98
1.4247-1.46330.25511410.22362151X-RAY DIFFRACTION99
1.4633-1.50630.24881490.20782181X-RAY DIFFRACTION99
1.5063-1.55490.2431420.20472165X-RAY DIFFRACTION99
1.5549-1.61050.21591380.20022174X-RAY DIFFRACTION99
1.6105-1.67490.23731460.19782186X-RAY DIFFRACTION100
1.6749-1.75110.23341420.18672178X-RAY DIFFRACTION100
1.7511-1.84340.24671370.19012195X-RAY DIFFRACTION100
1.8434-1.95890.21611490.18422187X-RAY DIFFRACTION100
1.9589-2.110.18421470.16632185X-RAY DIFFRACTION100
2.11-2.32220.19011440.16422195X-RAY DIFFRACTION100
2.3222-2.65780.21851440.17992186X-RAY DIFFRACTION100
2.6578-3.34690.19571470.1672217X-RAY DIFFRACTION100
3.3469-23.22720.15291450.15152196X-RAY DIFFRACTION98

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