› 1y75

X-ray diffraction
2.3Å resolution

A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge Cys 32- Cys 49 reveals recognition for N-acetylglucosmine

Released:
DOI: 10.2210/pdb1y75/pdb
PDB entry 1y75 coloured by chain, front view.
PDB entry 1y75 coloured by chain, side view.
PDB entry 1y75 coloured by chain, top view.
Source organism: Naja sagittifera
Primary publication:
Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 A resolution reveals the presence of a new PLA2-like protein with a novel cys 32-Cys 49 disulphide bridge with a bound sugar at the substrate-binding site.
Jabeen T, Singh N, Singh RK, Jasti J, Sharma S, Kaur P, Srinivasan A, Singh TP
Proteins 62 329-37 (2006)
PMID: 16287060

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-177134 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Acidic phospholipase A2 5 Chain: A
Molecule details ›
Chain: A
Length: 118 amino acids
Theoretical weight: 13.07 KDa
Source organism: Naja sagittifera
UniProt:
  • Canonical: Q5G291 (Residues: 8-125; Coverage: 95%)
Sequence domains: Phospholipase A2
Structure domains: Phospholipase A2 domain
Acidic phospholipase A2 6 Chain: B
Molecule details ›
Chain: B
Length: 118 amino acids
Theoretical weight: 12.71 KDa
Source organism: Naja sagittifera
UniProt:
  • Canonical: Q5G290 (Residues: 8-125; Coverage: 95%)
Sequence domains: Phospholipase A2
Structure domains: Phospholipase A2 domain

Ligands and Environments

2 bound ligands:
Ligand NAG 1 x NAG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P41212
Unit cell:
a: 77.656Å b: 77.656Å c: 68.424Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.256

Quick links

Citations

1 review citation

Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis.
Kang et al. (2011)
6 other articles

1 mention without citation

Electrostatic properties of protein-protein complexes.
Kundrotas et al. (2006)