2GDZ

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

PDB DOI: https://doi.org/10.2210/pdb2GDZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-03-17 Released: 2006-04-04
Deposition Author(s): Pilka, E.S., Guo, K., Kavanagh, K., Von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.212
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

High-Affinity Inhibitors of Human NAD-Dependent 15-Hydroxyprostaglandin Dehydrogenase: Mechanisms of Inhibition and Structure-Activity Relationships.

Niesen, F.H., Schultz, L., Jadhav, A., Bhatia, C., Guo, K., Maloney, D.J., Pilka, E.S., Wang, M., Oppermann, U., Heightman, T.D., Simeonov, A.

(2010) PLoS One 5: e13719-e13719

PubMed: 21072165 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0013719
Primary Citation of Related Structures:
2GDZ

PubMed Abstract:
15-Hydroxyprostaglandin dehydrogenase (15-PGDH, EC 1.1.1.141) is the key enzyme for the inactivation of prostaglandins, regulating processes such as inflammation or proliferation. The anabolic pathways of prostaglandins, especially with respect to regulation of the cyclooxygenase (COX) enzymes have been studied in detail; however, little is known about downstream events including functional interaction of prostaglandin-processing and -metabolizing enzymes. High-affinity probes for 15-PGDH will, therefore, represent important tools for further studies.

Organizational Affiliation

Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 29.84 kDa
Atom Count: 2,400
Modelled Residue Count: 266
Deposited Residue Count: 267
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD+-dependent 15-hydroxyprostaglandin dehydrogenase	A	267	Homo sapiens	Mutation(s): 0 EC: 1.1.1.141
UniProt & NIH Common Fund Data Resources
Find proteins for P15428 (Homo sapiens) Explore P15428 Go to UniProtKB: P15428
PHAROS: P15428 GTEx: ENSG00000164120
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15428
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.212
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.54	α = 90
b = 49.54	β = 90
c = 195.771	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-04-04
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description