2DW1 Apoptosis, Toxin date Aug 02, 2006
title Crystal Structure Of Vap2 From Crotalus Atrox Venom (Form 2-
authors S.Takeda, T.Igarashi, S.Araki
compound source
Molecule: Catrocollastatin
Chain: A, B
Fragment: Residues 191-609
Synonym: Vap2, Vascular Apoptosis-Inducing Protein-2, Catrocollastatinvap2b
Organism_scientific: Crotalus Atrox
Organism_common: Western Diamondback Rattlesnake
Organism_taxid: 8730
symmetry Space Group: P 21 21 21
R_factor 0.227 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.670 118.180 138.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand BMA, CA, FUC, GM6, MAN, NAG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structures of catrocollastatin/VAP2B reveal a dynamic, modular architecture of ADAM/adamalysin/reprolysin family proteins., Igarashi T, Araki S, Mori H, Takeda S, FEBS Lett. 2007 May 29;581(13):2416-22. Epub 2007 Apr 30. PMID:17485084
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (2dw1.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (2dw1.pdb2.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 2DW1
  • CSU: Contacts of Structural Units for 2DW1
  • Likely Quarternary Molecular Structure file(s) for 2DW1
  • Structure Factors (276 Kb)
  • Retrieve 2DW1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DW1 from S2C, [Save to disk]
  • Re-refined 2dw1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DW1 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 2DW1
  • 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 2DW1, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dw1_B] [2dw1] [2dw1_A]
  • SWISS-PROT database: [Q90282]
  • Domain organization of [Q90282_CROAT] by SWISSPFAM
  • Domains found in 2DW1: [ACR] [DISIN ] by SMART
  • Other resources with information on 2DW1
  • Community annotation for 2DW1 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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