2E3X

Crystal structure of Russell's viper venom metalloproteinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of RVV-X: an example of evolutionary gain of specificity by ADAM proteinases.

Takeda, S., Igarashi, T., Mori, H.

(2007) FEBS Lett 581: 5859-5864

  • DOI: 10.1016/j.febslet.2007.11.062
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Russell's viper venom factor X activator (RVV-X) is a heterotrimeric metalloproteinase with a mammalian ADAM-like heavy chain and two lectin-like light chains. The crystal structure of RVV-X has been determined at 2.9 A resolution and shows a hook-sp ...

    Russell's viper venom factor X activator (RVV-X) is a heterotrimeric metalloproteinase with a mammalian ADAM-like heavy chain and two lectin-like light chains. The crystal structure of RVV-X has been determined at 2.9 A resolution and shows a hook-spanner-wrench-like architecture, in which the metalloproteinase/disintegrin region constitutes a hook, and the lectin-like domains constitute a handle. A 6.5nm separation between the catalytic site and a putative exosite suggests a docking model for factor X. The structure provides a typical example of the molecular evolution of multi-subunit proteins and insights into the molecular basis of target recognition and proteolysis by ADAM/adamalysin/reprolysin proteinases.

    Organizational Affiliation: 

    Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565, Japan. stakeda@ri.ncvc.go.jp



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X-activating enzyme heavy chainA427Daboia siamensisMutation(s): 0 
EC: 3.4.24.58
Find proteins for Q7LZ61 (Daboia siamensis)
Explore Q7LZ61 
Go to UniProtKB:  Q7LZ61
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X-activating enzyme light chain 2B134Daboia siamensisMutation(s): 0 
Gene Names: LC2
Find proteins for Q4PRD2 (Daboia siamensis)
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Go to UniProtKB:  Q4PRD2
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X-activating enzyme light chain 1C122Daboia siamensisMutation(s): 0 
Gene Names: LC1
Find proteins for Q4PRD1 (Daboia siamensis)
Explore Q4PRD1 
Go to UniProtKB:  Q4PRD1
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  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2 N-Glycosylation
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
4 N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GM6
Query on GM6
Download CCD File 
A
3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
C20 H28 N4 O4
NITYDPDXAAFEIT-DYVFJYSZSA-N		 Ligand Interaction
NAG
Query on NAG
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A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.35α = 90
b = 91.73β = 90
c = 152.93γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary