› 4imn

X-ray diffraction
2.09Å resolution

Crystal structure of wild type human Lipocalin PGDS bound with PEG MME 2000

Released:
DOI: 10.2210/pdb4imn/pdb
PDB entry 4imn coloured by chain, front view.
PDB entry 4imn coloured by chain, side view.
PDB entry 4imn 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

1 bound ligand:
Ligand 1PG 1 x 1PG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P212121
Unit cell:
a: 36.413Å b: 56.413Å c: 72.988Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.212
Expression system: Escherichia coli

Quick links

Citations

9 citation in other articles

Abundant neuroprotective chaperone Lipocalin-type prostaglandin D synthase (L-PGDS) disassembles the Amyloid-β fibrils.
Kannaian et al. (2019)
8 more

4 mentions without citation

Molecular mechanisms of amyloid disaggregation.
Low et al. (2022)
3 more