[English] 日本語
Yorodumi
- PDB-5dp6: Crystal Structure of EV71 3C Proteinase in complex with compound 7 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...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 / 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 / ATP hydrolysis 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more