2DW0

Crystal structure of VAP2 from Crotalus atrox venom (Form 2-1 crystal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report



Literature

Crystal structures of catrocollastatin/VAP2B reveal a dynamic, modular architecture of ADAM/adamalysin/reprolysin family proteins

Igarashi, T.Araki, S.Mori, H.Takeda, S.

(2007) FEBS Lett 581: 2416-2422

  • DOI: 10.1016/j.febslet.2007.04.057
  • Primary Citation of Related Structures:  
    2DW2, 2DW1, 2DW0

  • PubMed Abstract: 
  • Catrocollastatin/vascular apoptosis-inducing protein (VAP)2B is a metalloproteinase from Crotalus atrox venom, possessing metalloproteinase/disintegrin/cysteine-rich (MDC) domains that bear the typical domain architecture of a disintegrin and metallo ...

    Catrocollastatin/vascular apoptosis-inducing protein (VAP)2B is a metalloproteinase from Crotalus atrox venom, possessing metalloproteinase/disintegrin/cysteine-rich (MDC) domains that bear the typical domain architecture of a disintegrin and metalloproteinase (ADAM)/adamalysin/reprolysin family proteins. Here we describe crystal structures of catrocollastatin/VAP2B in three different crystal forms, representing the first reported crystal structures of a member of the monomeric class of this family of proteins. The overall structures show good agreement with both monomers of atypical homodimeric VAP1. Comparison of the six catrocollastatin/VAP2B monomer structures and the structures of VAP1 reveals a dynamic, modular architecture that may be important for the functions of ADAM/adamalysin/reprolysin family proteins.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom.
      Igarashi, T., Oishi, Y., Araki, S., Mori, H., Takeda, S.
      (2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 688
    • Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold
      Takeda, S., Igarashi, T., Mori, H., Araki, S.
      (2006) EMBO J 25: 2388
    • cDNA cloning and some additional peptide characterization of a single-chain vascular apoptosis-inducing protein, VAP2
      Masuda, S., Maeda, H., Miao, J.Y., Hayashi, H., Araki, S.
      (2007) Endothelium 14: 89
    • Two vascular apoptosis-inducing proteins from snake venom are members of the metalloprotease/disintegrin family
      Masuda, S., Hayashi, H., Araki, S.
      (1998) Eur J Biochem 253: 36

    Organizational Affiliation

    Department of Cardiac Physiology, National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CatrocollastatinAB419Crotalus atroxMutation(s): 0 
EC: 3.4.24
Find proteins for Q90282 (Crotalus atrox)
Explore Q90282 
Go to UniProtKB:  Q90282
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5 N-Glycosylation
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
6 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GM6
Query on GM6

Download CCD File 
A, B
3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
C20 H28 N4 O4
NITYDPDXAAFEIT-DYVFJYSZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.91α = 90
b = 137.95β = 91.52
c = 59.24γ = 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: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary