› 2gdz

X-ray diffraction
1.65Å resolution

Crystal structure of 15-hydroxyprostaglandin dehydrogenase type1, complexed with NAD+

Released:
DOI: 10.2210/pdb2gdz/pdb
PDB entry 2gdz coloured by chain, front view.
PDB entry 2gdz coloured by chain, side view.
PDB entry 2gdz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
High-affinity inhibitors of human NAD-dependent 15-hydroxyprostaglandin dehydrogenase: mechanisms of inhibition and structure-activity relationships.
Niesen FH, Schultz L, Jadhav A, Bhatia C, Guo K, Maloney DJ, Pilka ES, Wang M, Oppermann U, Heightman TD, Simeonov A
OpenAccess logo PLoS One 5 e13719 (2010)
PMID: 21072165

Function and Biology Details

Reactions catalysed: 
(5Z,13E,15S)-11-alpha,15-dihydroxy-9-oxoprost-5,13-dienoate + NAD(+) = (5Z,13E)-11-alpha-hydroxy-9,15-dioxoprost-5,13-dienoate + NADH
(15S)-15-hydroxy-5,8,11-cis-13-trans-icosatetraenoate + NAD(P)(+) = 15-oxo-5,8,11-cis-13-trans-icosatetraenoate + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147362 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
15-hydroxyprostaglandin dehydrogenase [NAD(+)] Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 29.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P15428 (Residues: 3-256; Coverage: 96%)
  • Best match: P15428-3 (Residues: 1-135)
Gene names: HPGD, PGDH1, SDR36C1
Sequence domains: short chain dehydrogenase
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAD 1 x NAD
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P41212
Unit cell:
a: 49.54Å b: 49.54Å c: 195.771Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.212
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Recent developments in the use of differential scanning fluorometry in protein and small molecule discovery and characterization.
Simeonov A. (2013)
1 more

18 mentions without citation

From structural biology to designing therapy for inborn errors of metabolism.
Yue WW. (2016)
17 more