1U73 | pdb_00001u73

Crystal structure of a Dimeric Acidic Platelet Aggregation Inhibitor and Hypotensive Phospholipase A2 from Bothrops jararacussu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.247 (Depositor) 
  • R-Value Work: 
    0.190 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1U73

This is version 1.4 of the entry. See complete history

Literature

Crystal structure of an acidic platelet aggregation inhibitor and hypotensive phospholipase A(2) in the monomeric and dimeric states: insights into its oligomeric state

Magro, A.J.Murakami, M.T.Marcussi, S.Soares, A.M.Arni, R.K.Fontes, M.R.

(2004) Biochem Biophys Res Commun 323: 24-31

  • DOI: https://doi.org/10.1016/j.bbrc.2004.08.046
  • Primary Citation Related Structures: 
    1U73, 1UMV

  • PubMed Abstract: 

    Phospholipases A2 belong to the superfamily of proteins which hydrolyzes the sn-2 acyl groups of membrane phospholipids to release arachidonic acid and lysophospholipids. An acidic phospholipase A2 isolated from Bothrops jararacussu snake venom presents a high catalytic, platelet aggregation inhibition and hypotensive activities. This protein was crystallized in two oligomeric states: monomeric and dimeric. The crystal structures were solved at 1.79 and 1.90 angstroms resolution, respectively, for the two states. It was identified a Na+ ion at the center of Ca2+-binding site of the monomeric form. A novel dimeric conformation with the active sites exposed to the solvent was observed. Conformational states of the molecule may be due to the physicochemical conditions used in the crystallization experiments. We suggest dimeric state is one found in vivo.


  • Organizational Affiliation
    • Departamento de Física e Biofísica, Instituto de Biociências, UNESP, Botucatu-SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 27.4 kDa 
  • Atom Count: 2,281 
  • Modeled Residue Count: 244 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hypotensive phospholipase A2
A, B
122Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for Q8AXY1 (Bothrops jararacussu)
Explore Q8AXY1 
Go to UniProtKB:  Q8AXY1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8AXY1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.247 (Depositor) 
  • R-Value Work:  0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.193α = 90
b = 63.136β = 102.3
c = 47.407γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary