1POC

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

• PDB DOI: https://doi.org/10.2210/pdb1POC/pdb

• Classification: HYDROLASE
• Organism(s): Apis mellifera
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1992-09-07 Released: 1993-10-31 
• Deposition Author(s): Scott, D.L., Otwinowski, Z., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

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: 2274788 
• DOI: https://doi.org/10.1126/science.2274788
• Primary Citation of Related Structures:  
  1POC


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.8 kDa 
• Atom Count: 1,177 
• Modelled Residue Count: 134 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	A	134	Apis mellifera	Mutation(s): 0  EC: 3.1.1.4 Membrane Entity: Yes
UniProt
Find proteins for P00630 (Apis mellifera) Explore P00630  Go to UniProtKB:  P00630

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GEL	C [auth A]	1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C20 H45 N O8 P2 RCCNUBYROFOKAU-HXUWFJFHSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 89.5	β = 90
c = 132.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROFFT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Scott, D.L., Otwinowski, Z., Sigler, P.B.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary