1MQT

Swine Vesicular Disease Virus coat protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


  • 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 co ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
A
283Swine vesicular disease virusGene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Go to UniProtKB:  Q8B8X4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyprotein Capsid Protein
B
261Swine vesicular disease virusGene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Go to UniProtKB:  Q8B8X4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyprotein Capsid Protein
C
238Swine vesicular disease virusGene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Go to UniProtKB:  Q8B8X4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Polyprotein Capsid Protein
D
68Swine vesicular disease virusGene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Go to UniProtKB:  Q8B8X4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPL
Query on SPL

Download SDF File 
Download CCD File 
A
OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
CERAMIDE
C26 H51 N O3
APDLCSPGWPLYEQ-WUBHUQEYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.257 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 318.350α = 90.00
b = 349.960β = 90.00
c = 371.720γ = 90.00
Software Package:
Software NamePurpose
DMmodel building
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance