1IJL | pdb_00001ijl

Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus

• PDB DOI: https://doi.org/10.2210/pdb1IJL/pdb

• Classification: HYDROLASE
• Organism(s): Deinagkistrodon acutus
• Mutation(s): No 


• Deposited: 2001-04-27 Released: 2001-12-28 
• Deposition Author(s): Gu, L., Zhang, H., Song, S., Zhou, Y., Lin, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 

Starting Model: experimental

Literature

Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus.

Gu, L., Zhang, H., Song, S., Zhou, Y., Lin, Z.

(2002) Acta Crystallogr D Biol Crystallogr 58: 104-110

• PubMed: 11752784 
• DOI: https://doi.org/10.1107/s0907444901018170
• Primary Citation Related Structures: 
  1IJL


• PubMed Abstract: 
  

  An acidic phospholipase A(2) was purified from Deinagkistrodon acutus (Agkistrodon acutus) which displays an inhibitory effect on platelet aggregation. The three-dimensional structure of the enzyme was determined by molecular replacement at 2.6 A resolution with a crystallographic R factor of 18.40% (R(free) = 22.50%) and reasonable stereochemistry. Two molecules in the asymmetric unit form a dimer and the dimer formation accompanies a significant conformational adaptation of segment 14-23, a constituent of the 'interface recognition site' (IRS). This probably reflects the inherent structural flexibility of the IRS. The possible expansion of the site for inhibiting platelet aggregation as proposed previously [Wang et al. (1996), J. Mol. Biol. 255, 669-676] is discussed.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.33 kDa 
• Atom Count: 2,020 
• Modeled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	A, B	123	Deinagkistrodon acutus	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for Q7SID6 (Deinagkistrodon acutus) Explore Q7SID6  Go to UniProtKB:  Q7SID6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.71	α = 90
b = 38	β = 99.35
c = 69.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-28 
Deposition Author(s): Gu, L., Zhang, H., Song, S., Zhou, Y., Lin, Z.

Revision History  

• Version 1.0: 2001-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary