1VCY Toxin date Mar 17, 2004
title Vva2 Isoform
authors S.C.Lin, Y.C.Lo, J.Y.Lin, Y.C.Liaw
compound source
Molecule: Volvatoxin A2
Chain: A
Other_details: Isoform
 Organism_scientific: Volvariella Volvacea
Organism_taxid: 36659
symmetry Space Group: P 42 2 2
R_factor 0.225 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.107 56.107 132.427 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand MLI enzyme
related structures by homologous chain: 1VGF
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures and electron micrographs of fungal volvatoxin A2., Lin SC, Lo YC, Lin JY, Liaw YC, J Mol Biol 2004 Oct 15;343(2):477-91. PMID:15451675
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (1vcy.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 1VCY
  • CSU: Contacts of Structural Units for 1VCY
  • Likely Quarternary Molecular Structure file(s) for 1VCY
  • Structure Factors (87 Kb)
  • Retrieve 1VCY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VCY from S2C, [Save to disk]
  • Re-refined 1vcy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VCY in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1VCY
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VCY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vcya_, region A [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vcy_A] [1vcy]
  • SWISS-PROT database: [Q6USC4]
  • Belongs to the cytolytic delta endotoxin (cyt1/2) family according to TCDB.
  • Domain organization of [Q6USC4_9AGAR] by SWISSPFAM
    • Other resources with information on 1VCY
  • Community annotation for 1VCY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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