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), 0.232 (DCC)
R-Value Work:
0.246 (Depositor), 0.246 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 21871889 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2011.08.022
Primary Citation 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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18965
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0G6 Query on 0G6 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.328 (Depositor), 0.232 (DCC)
R-Value Work: 0.246 (Depositor), 0.246 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Nakayama, D.

Ben Ammar, Y.

Takeda, S.

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