1POB

CRYSTAL STRUCTURE OF COBRA-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: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

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

(1990) Science 250: 1560-1563

  • DOI: 10.1126/science.2274787
  • Primary Citation of Related Structures:  
    1POB

  • PubMed Abstract: 
  • The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase A2 (PLA2) from Naja naja atra venom has been solved and refined to a resolution of 2.0 angstroms. The identical stereochemistry of the two complexes that comprise the crystal's asymmetric unit indicates both the manner in which the transition state is stabilized and how the hydrophobic fatty acyl chains of the substrate are accommodated by the enzyme during interfacial catalysis ...

    The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase A2 (PLA2) from Naja naja atra venom has been solved and refined to a resolution of 2.0 angstroms. The identical stereochemistry of the two complexes that comprise the crystal's asymmetric unit indicates both the manner in which the transition state is stabilized and how the hydrophobic fatty acyl chains of the substrate are accommodated by the enzyme during interfacial catalysis. The critical features that suggest the chemistry of binding and catalysis are the same as those seen in the crystal structure of a similar complex formed with the evolutionarily distant bee-venom PLA2.


    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 A2A, B118Naja atraMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P00598 (Naja atra)
Explore P00598 
Go to UniProtKB:  P00598
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00598
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 
E [auth A],
H [auth B]
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 
C [auth A],
D [auth A],
F [auth B],
G [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.6α = 90
b = 73.5β = 90
c = 181.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




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, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description