Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.23 kDa 
• Atom Count: 1067 
• Modelled Residue Count: 118 
• Deposited Residue Count: 118 
• Unique protein chains: 1

1POA

INTERFACIAL CATALYSIS: THE MECHANISM OF PHOSPHOLIPASE A2

• PDB DOI: 10.2210/pdb1POA/pdb

• Classification: HYDROLASE
• Organism(s): Naja atra
• 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: 1.50 Å
• R-Value Work: 0.143 
• R-Value Observed: 0.143 

Literature

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: 1541-1546

• PubMed: 2274785 
• DOI: 10.1126/science.2274785
• Primary Citation of Related Structures:  
  1POA


• PubMed Abstract: 
  

A chemical description of the action of phospholipase A2 (PLA2) can now be inferred with confidence from three high-resolution x-ray crystal structures. The first is the structure of the PLA2 from the venom of the Chinese cobra (Naja naja atra) in a complex with a phosphonate transition-state analogue. This enzyme is typical of a large, well-studied homologous family of PLA2S. The second is a similar complex with the evolutionarily distant bee-venom PLA2. The third structure is the uninhibited PLA2 from Chinese cobra venom. Despite the different molecular architectures of the cobra and bee-venom PLA2s, the transition-state analogue interacts in a nearly identical way with the catalytic machinery of both enzymes. The disposition of the fatty-acid side chains suggests a common access route of the substrate from its position in the lipid aggregate to its productive interaction with the active site. Comparison of the cobra-venom complex with the uninhibited enzyme indicates that optimal binding and catalysis at the lipid-water interface is due to facilitated substrate diffusion from the interfacial binding surface to the catalytic site rather than an allosteric change in the enzyme's structure. However, a second bound calcium ion changes its position upon the binding of the transition-state analogue, suggesting a mechanism for augmenting the critical electrophile.

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Related Citations: 

• 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

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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	118	Naja atra	Mutation(s): 0  EC: 3.1.1.4 Membrane Entity: Yes
UniProt
Find proteins for P00598 (Naja atra) Explore P00598  Go to UniProtKB:  P00598

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 0.143 
• R-Value Observed: 0.143 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93	α = 90
b = 93	β = 90
c = 22.2	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): 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