1POC

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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 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

  • DOI: 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2A134Apis melliferaMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for P00630 (Apis mellifera)
Explore P00630 
Go to UniProtKB:  P00630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00630
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEL
Query on GEL
Download Ideal Coordinates CCD File 
C [auth A]1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C20 H45 N O8 P2
RCCNUBYROFOKAU-HXUWFJFHSA-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 Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.5α = 90
b = 89.5β = 90
c = 132.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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