2DW0

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2007.04.057
Primary Citation of Related Structures:
2DW0, 2DW1, 2DW2

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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 97.04 kDa
Atom Count: 7,292
Modelled Residue Count: 828
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q90282
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G83473RC GlyCosmos: G83473RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G35619UY GlyCosmos: G35619UY GlyGen: G35619UY

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GM6 Query on GM6 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B]	I [auth A], N [auth B]	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE C₂₀ H₂₈ N₄ O₄ NITYDPDXAAFEIT-DYVFJYSZSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-07-10

Deposition Author(s):

Takeda, S.

Igarashi, T.

Araki, S.

Revision History (Full details and data files)

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
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary