3SBK | pdb_00003sbk

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

• PDB DOI: https://doi.org/10.2210/pdb3SBK/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Daboia siamensis
• Mutation(s): No 


• Deposited: 2011-06-05 Released: 2011-09-07 
• Deposition Author(s): Nakayama, D., Ben Ammar, Y., Takeda, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.328 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

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

• PubMed: 21871889 
• DOI: https://doi.org/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 1.8Å 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.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.64 kDa 
• Atom Count: 1,878 
• Modelled Residue Count: 234 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vipera russelli proteinase RVV-V gamma	A	234	Daboia siamensis	Mutation(s): 0  EC: 3.4.21.95
UniProt
Find proteins for P18965 (Daboia siamensis) Explore P18965  Go to UniProtKB:  P18965
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0G6	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
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	C [auth A]	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.328 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.233	α = 90
b = 77.233	β = 90
c = 168.433	γ = 120

Software Package:

Software Name	Purpose
SPACE	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Nakayama, D., Ben Ammar, Y., Takeda, S.

Revision History  

• 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
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-13
  Changes: Structure summary