Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.45 kDa 
• Atom Count: 2136 
• Modelled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

1POB

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

• PDB DOI: 10.2210/pdb1POB/pdb

• Classification: HYDROLASE
• Organism(s): Naja atra
• Mutation(s): No 


• Deposited: 1992-09-07 Released: 1993-10-31 
• Deposition Author(s): White, S.P., 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: 0.179 
• R-Value Observed: 0.179 

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

• PubMed: 2274787 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	A, B	118	Naja atra	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P00598 (Naja atra) Explore P00598  Go to UniProtKB:  P00598

Small Molecules

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

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 = 34.6	α = 90
b = 73.5	β = 90
c = 181.6	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

• Deposited Date: 1992-09-07 
• Released Date: 1993-10-31 
Deposition Author(s): White, S.P., 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, Derived calculations, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description