Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97.04 kDa 
• Atom Count: 7292 
• Modelled Residue Count: 828 
• Deposited Residue Count: 838 
• Unique protein chains: 1

2DW0

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

• DOI: 10.2210/pdb2DW0/pdb

• Classification: APOPTOSIS, TOXIN
• Organism(s): Crotalus atrox
• Mutation(s): No 


• Deposited: 2006-08-02 Released: 2007-07-10 
• Deposition Author(s): Takeda, S., Igarashi, T., Araki, S.

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Experimental Data Snapshot

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

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

• PubMed: 17485084 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catrocollastatin	A, B	419	Crotalus atrox	Mutation(s): 0  EC: 3.4.24
UniProt
Find proteins for Q90282 (Crotalus atrox) Explore Q90282  Go to UniProtKB:  Q90282

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D 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
Glycosylation Resources
GlyTouCan:  G83473RC GlyCosmos:  G83473RC

Entity ID: 3
Molecule	Chains	Chain Length	2D 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
Glycosylation Resources
GlyTouCan:  G35619UY GlyCosmos:  G35619UY GlyGen:  G35619UY

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GM6 (Subject of Investigation/LOI)	I [auth A], N [auth B]	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE C20 H28 N4 O4 NITYDPDXAAFEIT-DYVFJYSZSA-N
ZN	E [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 56.91	α = 90
b = 137.95	β = 91.52
c = 59.24	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2006-08-02 
• Released Date: 2007-07-10 
Deposition Author(s): Takeda, S., Igarashi, T., Araki, S.

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