1ZL7

Crystal structure of catalytically-active phospholipase A2 with bound calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca(2+) free and bound states.

Murakami, M.T.Gabdoulkhakov, A.Genov, N.Cintra, A.C.Betzel, C.Arni, R.K.

(2006) Biochimie 88: 543-549

  • DOI: 10.1016/j.biochi.2005.10.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in t ...

    The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca(2+) free and bound states at 0.97 and 1.60 A resolutions, respectively. In the Ca(2+) bound state, the Ca(2+) ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca(2+), a water molecule occupies the position of the Ca(2+) ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation.


    Related Citations: 
    • Crystallization and high-resolution X-ray diffraction data collection of an Asp49 PLA2 from Bothrops jararacussu venom both in the presence and absence of Ca2+ ions.
      Murakami, M.T.,Michelan-Duarte, S.,Cintra, A.C.O.,Arni, R.K.
      (2004) Biochim.Biophys.Acta 1703: 79


    Organizational Affiliation

    Department of Physics, IBILCE/UNESP, Cristovão Colombo 2265, São José do Rio Preto, SP 15054-000, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypotensive phospholipase A2
A
122Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q8AXY1 (Bothrops jararacussu)
Go to UniProtKB:  Q8AXY1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 39.206α = 90.00
b = 53.218β = 90.00
c = 90.057γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description