1POC

CRYSTAL STRUCTURE OF BEE-VENOM PHOSPHOLIPASE A2 IN A COMPLEX WITH A TRANSITION-STATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue.

Scott, D.L.Otwinowski, Z.Gelb, M.H.Sigler, P.B.

(1990) Science 250: 1563-1566


  • PubMed Abstract: 
  • The 2.0 angstroms crystal structure of a complex containing bee-venom phospholipase A2 (PLA2) and a phosphonate transition-state analogue was solved by multiple isomorphous replacement. The electron-density map is sufficiently detailed to visualize t ...

    The 2.0 angstroms crystal structure of a complex containing bee-venom phospholipase A2 (PLA2) and a phosphonate transition-state analogue was solved by multiple isomorphous replacement. The electron-density map is sufficiently detailed to visualize the proximal sugars of the enzyme's N-linked carbohydrate and a single molecule of the transition-state analogue bound ot its active center. Although bee-venom PLA2 does not belong to the large homologous Class I/II family that encompasses most other well-studied PLA2s, there is segmental sequence similarity and conservation of many functional substructures. Comparison of the bee-venom enzyme with other phospholipase structures provides compelling evidence for a common catalytic mechanism.


    Related Citations: 
    • Interfacial Catalysis: The Mechanism of Phospholipase A2
      Scott, D.L.,White, S.P.,Otwinowski, Z.,Yuan, W.,Gelb, M.H.,Sigler, P.B.
      (1990) Science 250: 1541


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
134Apis melliferaMutation(s): 0 
EC: 3.1.1.4
Find proteins for P00630 (Apis mellifera)
Go to UniProtKB:  P00630
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GEL
Query on GEL

Download SDF File 
Download CCD File 
A
1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C20 H45 N O8 P2
RCCNUBYROFOKAU-HXUWFJFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.192 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 89.500α = 90.00
b = 89.500β = 90.00
c = 132.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
PROFFTrefinement
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance