1MQT

Swine Vesicular Disease Virus coat protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 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

  • DOI: 10.1128/jvi.77.18.9780-9789.2003
  • Primary Citation of 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 coxsac ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyprotein A283Swine vesicular disease virusMutation(s): 0 
Gene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyprotein Capsid Protein B261Swine vesicular disease virusMutation(s): 0 
Gene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyprotein Capsid Protein C238Swine vesicular disease virusMutation(s): 0 
Gene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Polyprotein Capsid Protein D68Swine vesicular disease virusMutation(s): 0 
Gene Names: 1ABCD
Find proteins for Q8B8X4 (Swine vesicular disease virus)
Explore Q8B8X4 
Go to UniProtKB:  Q8B8X4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPL
Query on SPL

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

Experimental Data

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

  • 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