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- PDB-5dp9: Crystal Structure of EV71 3C Proteinase in complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 5dp9
TitleCrystal Structure of EV71 3C Proteinase in complex with compound 9
Components3C proteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hand / foot and mouth disease / 3C proteinase / peptidomimetics / drug design / rupintrivir / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-5EX / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, C. / Zhang, L. / Li, P. / Cai, Q. / Peng, X. / Li, N. / Cai, Y. / Li, J. / Lin, T.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71
Authors: Wu, C. / Zhang, L. / Li, P. / Cai, Q. / Peng, X. / Yin, K. / Chen, X. / Ren, H. / Zhong, S. / Weng, Y. / Guan, Y. / Chen, S. / Wu, J. / Li, J. / Lin, T.
History
DepositionSep 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9042
Polymers21,3911
Non-polymers5131
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8390 Å2
Unit cell
Length a, b, c (Å)64.126, 65.234, 76.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21A-376-

HOH

31A-386-

HOH

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Components

#1: Protein 3C proteinase


Mass: 21391.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9XG43
#2: Chemical ChemComp-5EX / ethyl (2Z,4S)-4-[(N-{[(cyclobutylmethyl)amino](oxo)acetyl}-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate


Mass: 512.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.99 Å3/Da / Density % sol: 33.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100mM Tris, 25% PEG4000, 0.8M lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2013 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 11963 / % possible obs: 95.8 % / Redundancy: 3.7 % / Net I/σ(I): 5.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GHQ

4ghq


Resolution: 1.9→45.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.683 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29268 615 4.9 %RANDOM
Rwork0.24232 ---
obs0.24473 11963 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.329 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å2-0 Å2-0 Å2
2--9.64 Å20 Å2
3----13.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 37 134 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191486
X-RAY DIFFRACTIONr_bond_other_d0.0010.021460
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9852013
X-RAY DIFFRACTIONr_angle_other_deg0.933350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95323.28164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82915253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4411512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4072.965727
X-RAY DIFFRACTIONr_mcbond_other1.3982.964726
X-RAY DIFFRACTIONr_mcangle_it2.1964.443908
X-RAY DIFFRACTIONr_mcangle_other2.1964.444909
X-RAY DIFFRACTIONr_scbond_it1.2983.089757
X-RAY DIFFRACTIONr_scbond_other1.2983.092758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0624.5831101
X-RAY DIFFRACTIONr_long_range_B_refined5.0128.0966249
X-RAY DIFFRACTIONr_long_range_B_other4.87827.9846169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.493 44 -
Rwork0.432 874 -
obs--97.87 %

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