› 5jat

X-ray diffraction
2.04Å resolution

Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered Through X-Ray Fragment Screening

Released:
DOI: 10.2210/pdb5jat/pdb
PDB entry 5jat coloured by chain, front view.
PDB entry 5jat coloured by chain, side view.
PDB entry 5jat coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.
Woolford AJ, Pero JE, Aravapalli S, Berdini V, Coyle JE, Day PJ, Dodson AM, Grondin P, Holding FP, Lee LY, Li P, Manas ES, Marino J, Martin AC, McCleland BW, McMenamin RL, Murray CW, Neipp CE, Page LW, Patel VK, Potvain F, Rich S, Rivero RA, Smith K, Somers DO, Trottet L, Velagaleti R, Williams G, Xie R
J Med Chem 59 5356-67 (2016)
PMID: 27167608

Function and Biology Details

Reaction catalysed: 
1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171527 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Platelet-activating factor acetylhydrolase Chain: A
Molecule details ›
Chain: A
Length: 388 amino acids
Theoretical weight: 44.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13093 (Residues: 46-428; Coverage: 91%)
Gene names: PAFAH, PLA2G7
Sequence domains: Platelet-activating factor acetylhydrolase, isoform II
Structure domains: alpha/beta hydrolase

Ligands and Environments

3 bound ligands:
Ligand CL 1 x CL
Ligand DMS 1 x DMS
Ligand 6HR 1 x 6HR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: C2
Unit cell:
a: 100.06Å b: 91.067Å c: 51.442Å
α: 90° β: 111.72° γ: 90°
R-values:
R R work R free
0.142 0.14 0.199
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Small-molecule inhibitors as potential therapeutics and as tools to understand the role of phospholipases A2.
Nikolaou et al. (2019)
3 more

1 mention without citation

Lipoprotein-associated phospholipase A2: The story continues.
Huang et al. (2020)