3SBK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    3S9A, 3S9B, 3S9C, 3SBK

  • 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 FV) determined at 1 ...

    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 Struct Biol Cryst Commun 65: 1306

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vipera russelli proteinase RVV-V gammaA234Daboia siamensisMutation(s): 0 
EC: 3.4.21.95
UniProt
Find proteins for P18965 (Daboia siamensis)
Explore P18965 
Go to UniProtKB:  P18965
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6 (Subject of Investigation/LOI)
Query on 0G6

Download Ideal Coordinates CCD File 
C [auth A]D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
C [auth A]D-Phe-Pro-Arg-CH2ClPeptide-like /  Inhibitor  Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.233α = 90
b = 77.233β = 90
c = 168.433γ = 120
Software Package:
Software NamePurpose
SPACEdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2013-07-03
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary