› 1gmz

X-ray diffraction
2.4Å resolution

Crystal structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai.

Released:
DOI: 10.2210/pdb1gmz/pdb
PDB entry 1gmz coloured by chain, front view.
PDB entry 1gmz coloured by chain, side view.
PDB entry 1gmz coloured by chain, top view.
Source organism: Bothrops pirajai
Primary publication:
The structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possiblerelationship to cooperative substrate binding.
Rigden DJ, Hwa LW, Marangoni S, Toyama MH, Polikarpov I
Acta Crystallogr D Biol Crystallogr 59 255-62 (2003)
PMID: 12554936

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157690 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Basic phospholipase A2 homolog piratoxin-3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 122 amino acids
Theoretical weight: 13.86 KDa
Source organism: Bothrops pirajai
UniProt:
  • Canonical: P58464 (Residues: 1-57, 58-81, 82-112, 113-120; Coverage: 99%)
Sequence domains: Phospholipase A2
Structure domains: Phospholipase A2 domain

Ligands and Environments

1 bound ligand:
Ligand IPA 2 x IPA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE D03B-MX1
Spacegroup: C2
Unit cell:
a: 61.019Å b: 100.937Å c: 48.333Å
α: 90° β: 123.76° γ: 90°
R-values:
R R work R free
0.201 0.201 0.255

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Citations

11 citation in other articles

Venom phospholipases A2 of bamboo viper (Trimeresurus stejnegeri): molecular characterization, geographic variations and evidence of multiple ancestries.
Tsai et al. (2004)
10 more

5 mentions without citation

An evolutionary conserved Hexim1 peptide binds to the Cdk9 catalytic site to inhibit P-TEFb.
Kobbi et al. (2016)
4 more