› 2dw1

X-ray diffraction
2.5Å resolution

Crystal structure of VAP2 from Crotalus atrox venom (Form 2-2 crystal)

Released:
DOI: 10.2210/pdb2dw1/pdb
PDB entry 2dw1 coloured by chain, front view.
PDB entry 2dw1 coloured by chain, side view.
PDB entry 2dw1 coloured by chain, top view.
Source organism: Crotalus atrox
Primary publication:
Crystal 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 581 2416-22 (2007)
PMID: 17485084

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187443 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Zinc metalloproteinase-disintegrin-like VAP2B Chains: A, B
Molecule details ›
Chains: A, B
Length: 419 amino acids
Theoretical weight: 46.91 KDa
Source organism: Crotalus atrox
UniProt:
  • Canonical: Q90282 (Residues: 191-609; Coverage: 71%)
Sequence domains:
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
3 bound ligands:
Ligand CA 6 x CA
Ligand ZN 2 x ZN
Ligand GM6 2 x GM6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 57.67Å b: 118.18Å c: 138.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.227 0.286

Quick links

Citations

15 review citations

The ADAM metalloproteinases.
Edwards et al. (2008)
14 more

2 mentions without citation

Snake Venom Metalloproteinases (SVMPs): A structure-function update.
Olaoba et al. (2020)
1 more