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- PDB-5dp4: Crystal Structure of EV71 3C Proteinase in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 5dp4
TitleCrystal Structure of EV71 3C Proteinase in complex with compound 3
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-5E8 / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)87,0568
Polymers85,5664
Non-polymers1,4904
Water6,539363
1
A: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7642
Polymers21,3911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7642
Polymers21,3911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7642
Polymers21,3911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7642
Polymers21,3911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.894, 75.456, 128.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 180 / Label seq-ID: 1 - 181

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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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-5E8 / ethyl (2Z,4S)-4-{[(2S)-2-methyl-3-phenylpropanoyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate


Mass: 372.458 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.94 Å3/Da / Density % sol: 32.25 %
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: Jan 20, 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: 2.21→50 Å / Num. obs: 29625 / % possible obs: 98 % / Redundancy: 6.1 % / Net I/σ(I): 13.3
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.9 / % possible all: 88.4

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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: 2.21→49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.765 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1582 5.1 %RANDOM
Rwork0.2121 ---
obs0.2145 29625 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.7 Å2 / Biso mean: 18.831 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20 Å2
2---5.37 Å2-0 Å2
3---6.83 Å2
Refinement stepCycle: final / Resolution: 2.21→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 108 363 6075
Biso mean--26.85 24.39 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195828
X-RAY DIFFRACTIONr_bond_other_d0.0080.025704
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9787888
X-RAY DIFFRACTIONr_angle_other_deg1.381313084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.923.71248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03415988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9031540
X-RAY DIFFRACTIONr_chiral_restr0.10.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216548
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021352
X-RAY DIFFRACTIONr_mcbond_it1.4391.6792892
X-RAY DIFFRACTIONr_mcbond_other1.4351.6782891
X-RAY DIFFRACTIONr_mcangle_it2.2432.5133608
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A114050.09
12B114050.09
21A114770.09
22C114770.09
31A117100.05
32D117100.05
41B115800.06
42C115800.06
51B114110.09
52D114110.09
61C114320.09
62D114320.09
LS refinement shellResolution: 2.213→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 102 -
Rwork0.272 1837 -
all-1939 -
obs--84.75 %

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