1PSJ | pdb_00001psj

ACIDIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS

• PDB DOI: https://doi.org/10.2210/pdb1PSJ/pdb

• Classification: HYDROLASE
• Organism(s): Gloydius halys
• Mutation(s): No 


• Deposited: 1995-05-24 Released: 1996-07-11 
• Deposition Author(s): Wang, X.Q., Lin, Z.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.157 (Depositor) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution.

Wang, X.Q., Yang, J., Gui, L.L., Lin, Z.J., Chen, Y.C., Zhou, Y.C.

(1996) J Mol Biology 255: 669-676

• PubMed: 8636969 
• DOI: https://doi.org/10.1006/jmbi.1996.0054
• Primary Citation Related Structures: 
  1PSJ


• PubMed Abstract: 
  

  The crystal structure of acidic phospholipase A2 from the venom of Agkistrodon halys pallas has been determined by molecular replacement at 2.0 A resolution to a crystallographic R-factor of 0.157. The overall structure of the molecule is very similar to those of other phospholipase A2 species of known structure. The catalytic site, the hydrophobic channel and the N-terminal region show greatest structural conservation. The Ca(2+)-binding region has a conformation that resembles closely that of bovine PLA2 rather than Crotalus atrox PLA2. Compared with other PLA2 species, the conformation of the C-terminal ridge shows significant difference due to the insertion of two residues. A unique aromatic patch appears on one face of the molecules, surrounded by two acidic residues, the relevant features of this structure and their possible biological implications are discussed.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Academia Sinica, Beijing, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.03 kDa 
• Atom Count: 1,104 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	A	124	Gloydius halys	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P14418 (Gloydius halys) Explore P14418  Go to UniProtKB:  P14418

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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 Free:  0.228 (Depositor) 
• R-Value Work:  0.157 (Depositor) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.57	α = 90
b = 83.57	β = 90
c = 32.72	γ = 120

Software Package:

Software Name	Purpose
XENGEN	data collection
XENGEN	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-07-11 
Deposition Author(s): Wang, X.Q., Lin, Z.J.

Revision History  

• Version 1.0: 1996-07-11
  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: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-11-06
  Changes: Structure summary