ISDA: 3S9B

Deposition Date 2011-06-01

Release Date 2011-09-07

Last Version Date 2024-10-30

Entry Detail

PDB ID:

3S9B

Keywords:

HYDROLASE

Title:

Russell's viper venom serine proteinase, RVV-V (open-form)

Biological Source:

Source Organism:

Daboia russellii siamensis (Taxon ID: 343250)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.90 Å

R-Value Free:

0.21

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 65 2 2

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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

NAG

Primary Citation

Structural basis of coagulation factor V recognition for cleavage by RVV-V

Nakayama, D, Ben Ammar, Y, Miyata, T, Takeda, S, Nakayama, D, Ben Ammar, Y, Takeda, S.Show

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.

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Disease

Primary Citation of related structures