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- PDB-5dp3: Crystal Structure of EV71 3C Proteinase in complex with compound 2 -

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Basic information

Entry
Database: PDB / ID: 5dp3
TitleCrystal Structure of EV71 3C Proteinase in complex with compound 2
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-5GH / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)21,7502
Polymers21,3911
Non-polymers3581
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8450 Å2
Unit cell
Length a, b, c (Å)64.623, 64.845, 75.366
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-371-

HOH

31A-389-

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-5GH / ethyl (4S)-5-[(3S)-2-oxopyrrolidin-3-yl]-4-[(3-phenylpropanoyl)amino]pent-2-enoate


Mass: 358.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 33.35 %
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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2013 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 10155 / % possible obs: 98.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.108 / Χ2: 1.459 / Net I/av σ(I): 15.737 / Net I/σ(I): 8.9 / Num. measured all: 42175
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.0940.4455101.39799.6
2.09-2.124.30.4144911.346100
2.12-2.164.20.3585111.48899.4
2.16-2.214.40.3564891.59699.8
2.21-2.264.40.3114971.54699.8
2.26-2.314.20.2875201.57299.4
2.31-2.374.40.2794921.59999.6
2.37-2.434.30.2455101.60999.4
2.43-2.54.40.2365001.68298.8
2.5-2.584.40.2115101.699.8
2.58-2.684.30.175131.46599.6
2.68-2.784.30.1494891.43499
2.78-2.914.20.1265131.44699.6
2.91-3.064.20.115081.5398.6
3.06-3.254.10.0845131.37197.9
3.25-3.5140.0734971.40497.3
3.51-3.863.90.0635031.44596.2
3.86-4.423.70.0535081.38997.3
4.42-5.563.60.0525171.07995.9
5.56-5040.0475641.07598.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GHQ

4ghq


Resolution: 2.05→45.77 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / SU B: 6.244 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2943 491 4.8 %RANDOM
Rwork0.2237 ---
obs0.227 9647 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 25.013 Å2 / Biso min: 2.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0 Å2
2--0.88 Å20 Å2
3----1.74 Å2
Refinement stepCycle: final / Resolution: 2.05→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 11 131 1543
Biso mean--42.81 31.87 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191449
X-RAY DIFFRACTIONr_bond_other_d0.0020.021422
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9661963
X-RAY DIFFRACTIONr_angle_other_deg0.92333261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15923.49263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90915250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0631511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
X-RAY DIFFRACTIONr_mcbond_it2.2072.354725
X-RAY DIFFRACTIONr_mcbond_other2.1792.352724
X-RAY DIFFRACTIONr_mcangle_it3.3783.523905
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 30 -
Rwork0.247 696 -
all-726 -
obs--98.37 %

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