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- PDB-5dp6: Crystal Structure of EV71 3C Proteinase in complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 5dp6
TitleCrystal Structure of EV71 3C Proteinase in complex with compound 7
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 / ribonucleoside triphosphate phosphatase 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 / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / ribonucleoside triphosphate phosphatase 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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-5EB / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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 30, 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
B: 3C proteinase
C: 3C proteinase
D: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5056
Polymers85,5664
Non-polymers9392
Water00
1
A: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8612
Polymers21,3911
Non-polymers4701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8612
Polymers21,3911
Non-polymers4701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)21,3911
Polymers21,3911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)21,3911
Polymers21,3911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.840, 85.709, 101.315
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 proteinase


Mass: 21391.482 Da / Num. of mol.: 4
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-5EB / ethyl (2Z,4S)-4-{[N-(3-cyclopropylpropanoyl)-L-phenylalanyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate


Mass: 469.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H35N3O5
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: 2.35 Å3/Da / Density % sol: 47.61 %
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: 3→50 Å / Num. obs: 14849 / % possible obs: 96.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.148 / Χ2: 1.454 / Net I/av σ(I): 12.325 / Net I/σ(I): 8.1 / Num. measured all: 71093
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.054.90.8797430.93498
3.05-3.114.90.6897191.02998.5
3.11-3.174.90.6227491.08396.9
3.17-3.234.90.5067441.05398.8
3.23-3.350.3737301.13597.9
3.3-3.384.90.3297381.31596.9
3.38-3.464.90.2897251.41998
3.46-3.564.90.2457531.52498.2
3.56-3.664.90.2297481.71297
3.66-3.784.90.1927111.80296.6
3.78-3.914.90.1847431.53796.7
3.91-4.074.90.1677371.67496.6
4.07-4.264.80.1327391.77296.3
4.26-4.484.60.117371.9396.8
4.48-4.764.70.0937381.7495.2
4.76-5.134.70.097361.54896.2
5.13-5.644.50.0897451.44795.6
5.64-6.464.80.0897501.46195.9
6.46-8.134.70.0827671.4895.4
8.13-504.10.0737971.60792.4

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Processing

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

4ghq


Resolution: 3.01→42.89 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.852 / SU B: 21.583 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 731 4.9 %RANDOM
Rwork0.2287 ---
obs0.2311 14092 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 235.87 Å2 / Biso mean: 91.206 Å2 / Biso min: 24.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å2-0 Å2
2---0.13 Å20 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 3.01→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 68 0 5621
Biso mean--55.15 --
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195734
X-RAY DIFFRACTIONr_bond_other_d0.0070.025610
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9687763
X-RAY DIFFRACTIONr_angle_other_deg1.589312865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0325712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39323.71248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85315976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4981540
X-RAY DIFFRACTIONr_chiral_restr0.0710.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216459
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021337
X-RAY DIFFRACTIONr_mcbond_it4.918.9022860
X-RAY DIFFRACTIONr_mcbond_other4.9118.92859
X-RAY DIFFRACTIONr_mcangle_it8.07213.3443568
LS refinement shellResolution: 3.005→3.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 46 -
Rwork0.274 933 -
all-979 -
obs--87.33 %

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