3SBK image
Deposition Date 2011-06-05
Release Date 2011-09-07
Last Version Date 2024-11-13
Entry Detail
PDB ID:
3SBK
Keywords:
HYDROLASE/HYDROLASE INHIBITOR
Title:
Russell's viper venom serine proteinase, RVV-V (PPACK-bound form)
Biological Source:
Source Organism:
Daboia russellii siamensis (Taxon ID: 343250)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.55 Å
R-Value Free:
0.32
R-Value Work:
0.24
R-Value Observed:
0.25
Space Group:
P 65 2 2
3SBK validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Vipera russelli proteinase RVV-V gamma
Chain IDs:A
Chain Length:234
Number of Molecules:1
Biological Source:Daboia russellii siamensis
UniProt ID:P18965 Pfam ID:PF00089 EC:3.4.21.95
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Ligand Molecules
0G6
NAG
Peptide-like Molecules
PRD_000020
Primary Citation
Structural basis of coagulation factor V recognition for cleavage by RVV-V
Febs Lett. 585 3020 3025 (2011)
PMID: 21871889 DOI: 10.1016/j.febslet.2011.08.022

Abstact

Russell's viper venom factor V (FV) activator (RVV-V) is a thrombin-like proteinase that specifically cleaves the Arg1545-Ser1546 bond of FV. Here we present the crystal structure of RVV-V in complex with the FV14 peptide (residues 1533-1546 of human FV) determined at 1.8Å resolution. The structure reveals multiple interactions between RVV-V and the seven residues, Ile1539 (P(7))-Arg1545 (P(1)), of the cleaved substrate. Comparison with substrate-free structures reveals conformational changes of the RVV-V loops upon substrate binding, suggesting that the multiple interactions are mediated by an induced-fit mechanism. The results provide an explanation for the narrow specificity of RVV-V.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3S9A
3S9B
3S9C