3S9C

Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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

(2011) Febs Lett. 585: 3020-3025

  • DOI: 10.1016/j.febslet.2011.08.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of blood coagulation factor V-activating proteinase (RVV-V) from Russell's viper venom
      Nakayama, D.,Ben Ammar, Y.,Takeda, S.
      (2009) Acta Crystallogr.,Sect.F 65: 1306


    Organizational Affiliation

    Department of Cardiac Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vipera russelli proteinase RVV-V gamma
A
234Daboia siamensisMutation(s): 0 
EC: 3.4.21.95
Find proteins for P18965 (Daboia siamensis)
Go to UniProtKB:  P18965
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor V
B
14Homo sapiensMutation(s): 0 
Gene Names: F5
Find proteins for P12259 (Homo sapiens)
Go to Gene View: F5
Go to UniProtKB:  P12259
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BGC
Query on BGC

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A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GLC
Query on GLC

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A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 101.200α = 90.00
b = 101.200β = 90.00
c = 44.200γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references