1O2E

Structure of the triple mutant (K53,56,120M) + Anisic acid complex of phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of the free and anisic acid bound triple mutant of phospholipase A2.

Sekar, K.Vaijayanthi Mala, S.Yogavel, M.Velmurugan, D.Poi, M.J.Vishwanath, B.S.Gowda, T.V.Jeyaprakash, A.A.Tsai, M.D.

(2003) J.Mol.Biol. 333: 367-376

  • Primary Citation of Related Structures:  
  • Also Cited By: 2BAX, 2B96

  • PubMed Abstract: 
  • Phospholipase A2 catalyses the hydrolysis of the ester bond of 3-sn-phosphoglycerides. Here, we report the crystal structures of the free and anisic acid-bound triple mutant (K53,56,120M) of bovine pancreatic phospholipase A2. In the bound triple mut ...

    Phospholipase A2 catalyses the hydrolysis of the ester bond of 3-sn-phosphoglycerides. Here, we report the crystal structures of the free and anisic acid-bound triple mutant (K53,56,120M) of bovine pancreatic phospholipase A2. In the bound triple mutant structure, the small organic molecule p-anisic acid is found in the active site, and one of the carboxylate oxygen atoms is coordinated to the functionally important primary calcium ion. The other carboxylate oxygen atom is hydrogen bonded to the phenolic hydroxyl group of Tyr69. In addition, the bound anisic acid molecule replaces one of the functionally important water molecules in the active site. The residues 60-70, which are in a loop (surface loop), are disordered in most of the bovine pancreatic phospholipase A2 structures. It is interesting to note that these residues are ordered in the bound triple mutant structure but are disordered in the free triple mutant structure. The organic crystallization ingredient 2-methyl-2,4-pentanediol is found near the active site of the free triple mutant structure. The overall tertiary folding and stereochemical parameters for the final models of the free and anisic acid-bound triple mutant are virtually identical.


    Organizational Affiliation

    Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India. sekar@physics.iisc.ernet.in




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2
A
123Bos taurusMutation(s): 3 
Gene Names: PLA2G1B
EC: 3.1.1.4
Find proteins for P00593 (Bos taurus)
Go to Gene View: PLA2G1B
Go to UniProtKB:  P00593
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANN
Query on ANN

Download SDF File 
Download CCD File 
A
4-METHOXYBENZOIC ACID
P-ANISIC ACID
C8 H8 O3
ZEYHEAKUIGZSGI-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: 2.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 46.610α = 90.00
b = 46.610β = 90.00
c = 102.680γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description