Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94824.70 
• Atom Count: 6491 
• Residue Count: 838 
• Unique protein chains: 1

3DSL

The Three-dimensional Structure of Bothropasin, the Main Hemorrhagic Factor from Bothrops jararaca venom.

• DOI: 10.2210/pdb3DSL/pdb

• Classification: HYDROLASE
• Organism(s): Bothrops jararaca


• Deposited: 2008-07-13 Released: 2008-10-21 
• Deposition Author(s): Muniz, J.R.C., Ambrosio, A., Selistre-de-Araujo, H.S., Oliva, G., Garratt, R.C., Souza, D.H.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.294 
• R-Value Work: 0.210 

Literature

The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: Insights for a new classification of snake venom metalloprotease subgroups.

Muniz, J.R., Ambrosio, A.L., Selistre-de-Araujo, H.S., Cominetti, M.R., Moura-da-Silva, A.M., Oliva, G., Garratt, R.C., Souza, D.H.

(2008) Toxicon 52: 807-816

• PubMed: 18831982 
• DOI: 10.1016/j.toxicon.2008.08.021


• PubMed Abstract: 
  

Bothropasin is a 48kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys189 is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from PII SVMPs. The ECD motif is stabilized by the Cys277-Cys310 disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu276 of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other PIII SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other PIII members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain.

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Organizational Affiliation: 

Departamento de Física e Informática, Instituto de Física de São Carlos, USP, São Carlos-SP CEP 13560-970, Brazil.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Zinc metalloproteinase-disintegrin bothropasin	A, B	419	Bothrops jararaca	Mutation(s): 0  EC: 3.4.24.49
Find proteins for O93523 (Bothrops jararaca) Go to UniProtKB:  O93523

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
TRP	A	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
FLE	A	FUROYL-LEUCINE C11 H15 N O4 LXBURZIESWDWIV-QMMMGPOBSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.294 
• R-Value Work: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 73.757	α = 90.00
b = 100.271	β = 90.00
c = 133.237	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
CrystalClear	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-13 
• Released Date: 2008-10-21 
• Deposition Author(s): Muniz, J.R.C., Ambrosio, A., Selistre-de-Araujo, H.S., Oliva, G., Garratt, R.C., Souza, D.H.F.

Revision History 

• Version 1.0: 2008-10-21
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance