1BK9

PHOSPHOLIPASE A2 MODIFIED BY PBPB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • DOI: 10.1016/s0041-0101(97)00169-4
  • Primary Citation of Related Structures:  
    1BK9

  • 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 structure as an initial model and refined to a crystallographic R factor of 15 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2A124Gloydius halysMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P14418 (Gloydius halys)
Explore P14418 
Go to UniProtKB:  P14418
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBP (Subject of Investigation/LOI)
Query on PBP

Download Ideal Coordinates CCD File 
C [auth A]p-Bromophenacyl bromide
C8 H6 Br2 O
FKJSFKCZZIXQIP-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

Download Ideal Coordinates CCD File 
D [auth A]1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.82α = 90
b = 82.82β = 90
c = 32.8γ = 120
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-11-27
    Changes: Advisory, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary