› 4imo

X-ray diffraction
1.88Å resolution

Crystal structure of wild type human Lipocalin PGDS in complex with substrate analog U44069

Released:
DOI: 10.2210/pdb4imo/pdb
PDB entry 4imo coloured by chain, front view.
PDB entry 4imo coloured by chain, side view.
PDB entry 4imo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.
Lim SM, Chen D, Teo H, Roos A, Jansson AE, Nyman T, Trésaugues L, Pervushin K, Nordlund P
J Lipid Res 54 1630-1643 (2013)
PMID: 23526831

Function and Biology Details

Reaction catalysed: 
(5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154342 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prostaglandin-H2 D-isomerase Chain: A
Molecule details ›
Chain: A
Length: 176 amino acids
Theoretical weight: 19.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P41222 (Residues: 23-190; Coverage: 100%)
Gene names: PDS, PTGDS
Sequence domains: Lipocalin / cytosolic fatty-acid binding protein family
Structure domains: Lipocalin

Ligands and Environments

2 bound ligands:
Ligand PWZ 2 x PWZ
Ligand SCN 2 x SCN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P212121
Unit cell:
a: 36.24Å b: 56.38Å c: 72.92Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.189 0.242
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Molecular mechanisms of amyloid disaggregation.
Low et al. (2022)
10 other articles

1 mention without citation

Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.
Lim et al. (2013)