1BK9

PHOSPHOLIPASE A2 MODIFIED BY PBPB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide.

Zhao, H.Tang, L.Wang, X.Zhou, Y.Lin, Z.

(1998) Toxicon 36: 875-886


  • PubMed Abstract: 
  • The crystal structure of acidic phospholipase A2 (APLA2) from Agkistrodon halys pallas covalently modified by p-bromo-phenacyl-bromide (pBPB) was determined to a resolution of 2.0 A by an isomorphous difference Fourier method with the native APLA2 st ...

    The crystal structure of acidic phospholipase A2 (APLA2) from Agkistrodon halys pallas covalently modified by p-bromo-phenacyl-bromide (pBPB) was determined to a resolution of 2.0 A by an isomorphous difference Fourier method with the native APLA2 structure as an initial model and refined to a crystallographic R factor of 15.3%. The modified APLA2 structure is remarkably similar to that of the native one. Least-squares superposition of C alpha atoms of native and modified APLA2 results in a root-mean-square coordinate deviation of 0.243 A. The p-bromo-phenacyl group near the active site occupies a position similar to that in pBPB modified bovine pancreatic PLA2. The inhibitor covalently bound to the NDI atom of His48 fits well in the hydrophobic channel, forming extensive hydrophobic interactions with the surrounding residues, especially with the side chains of Phe5 and Cys45 and the main chain of Gly30. However, the inhibitor does not change the conformation of these residues except that Trp31 at the entrance of the hydrophobic channel moves slightly toward the inhibitor. Compared with native APLA2, the Ca2+-binding loop shows a little conformational change and a cation, probably Na+, occupies in the position of Ca2+. The binding of pBPB to APLA2 induce no other significant conformational changes in the enzyme molecule elsewhere.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
124Gloydius halysEC: 3.1.1.4
Find proteins for P14418 (Gloydius halys)
Go to UniProtKB:  P14418
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBP
Query on PBP

Download SDF File 
Download CCD File 
A
1-(4-BROMO-PHENYL)-ETHANONE
C8 H7 Br O
WYECURVXVYPVAT-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

Download SDF File 
Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-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 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.153 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 82.820α = 90.00
b = 82.820β = 90.00
c = 32.800γ = 120.00
Software Package:
Software NamePurpose
XENGENdata reduction
X-PLORrefinement
XENGENdata scaling
X-PLORmodel building
X-PLORphasing
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance