1MQT | pdb_00001mqt

Swine Vesicular Disease Virus coat protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.279 (Depositor) 
  • R-Value Work: 
    0.257 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

STRUCTURE OF SWINE VESICULAR DISEASE VIRUS: MAPPING OF CHANGES OCCURRING DURING ADAPTATION OF HUMAN COXSACKIE B5 VIRUS TO INFECT SWINE

Verdaguer, N., Jimenez-Clavero, M.A., Fita, I., Ley, V.

(2003) J Virol 77: 9780-9789

  • DOI: https://doi.org/10.1128/jvi.77.18.9780-9789.2003
  • Primary Citation Related Structures: 
    1MQT

  • PubMed Abstract: 

    The structure of swine vesicular disease virus (SVDV) was solved and refined at a 3.0-A resolution by X-ray crystallography to gain information about the role of sequence changes that occurred as this virus evolved from the parental human pathogen coxsackievirus B5 (CVB5). These amino acid substitutions can be clustered in five distinct regions: (i) the antigenic sites, (ii) the hydrophobic pocket of the VP1 beta-sandwich, (iii) the putative CAR binding site, (iv) the putative heparan sulfate binding site, and (v) the fivefold axis. The VP1 pocket is occupied by a branched pocket factor, apparently different from that present in the closely related virus CVB3 and in other picornaviruses. This finding may be relevant for the design of new antiviral compounds against this site. Density consistent with the presence of ions was observed on the fivefold and threefold axes. The structure also provided an accurate description of the putative receptor binding sites.

    • Organizational Affiliation: 
    • Institut de Biologia Molecular de Barcelona (CSIC), Jordi Girona 18-26, 08034-Barcelona, Spain. nvmcri@ibmb.csic.es

Macromolecule Content 

  • Total Structure Weight: 93.73 kDa 
  • Atom Count: 6,393 
  • Modeled Residue Count: 818 
  • Deposited Residue Count: 850 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyprotein283Swine vesicular disease virusMutation(s): 0 
UniProt
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B8X4
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyprotein Capsid Protein261Swine vesicular disease virusMutation(s): 0 
UniProt
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B8X4
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyprotein Capsid Protein238Swine vesicular disease virusMutation(s): 0 
UniProt
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B8X4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyprotein Capsid Protein68Swine vesicular disease virusMutation(s): 0 
UniProt
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B8X4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPL

Query on SPL


Download:Ideal Coordinates CCD File
E [auth A]OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
C26 H51 N O3
APDLCSPGWPLYEQ-WUBHUQEYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.279 (Depositor) 
  • R-Value Work:  0.257 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 318.35α = 90
b = 349.96β = 90
c = 371.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNSrefinement
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description