9MDH | pdb_00009mdh

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP and Indomethacin (Orthorhombic P form)

PDB DOI: https://doi.org/10.2210/pdb9MDH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-05 Released: 2025-12-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.203 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP and Indomethacin (Orthorhombic P form)

Lovell, S., Cooper, A., Liu, L., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 149.85 kDa
Atom Count: 10,592
Modeled Residue Count: 1,312
Deposited Residue Count: 1,324
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin reductase 1	A, B, C, D	331	Homo sapiens	Mutation(s): 1 Gene Names: PTGR1, LTB4DH EC: 1.3.1.48 (PDB Primary Data), 1.3.1.74 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14914 (Homo sapiens) Explore Q14914 Go to UniProtKB: Q14914
PHAROS: Q14914 GTEx: ENSG00000106853
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14914
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain P [auth A] SDF format, chain MA [auth D] SDF format, chain FA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain P [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain P [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain FA [auth C]	FA [auth C], MA [auth D], P [auth A], X [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain FA [auth C] Focus chain MA [auth D] Focus chain P [auth A] Focus chain X [auth B] Interactions & Density Focus chain FA [auth C] Focus chain MA [auth D] Focus chain P [auth A] Focus chain X [auth B]
IMN (Subject of Investigation/LOI) Query on IMN Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain O [auth A] SDF format, chain LA [auth D] SDF format, chain EA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain EA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain EA [auth C]	EA [auth C], LA [auth D], O [auth A], W [auth B]	INDOMETHACIN C₁₉ H₁₆ Cl N O₄ CGIGDMFJXJATDK-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain LA [auth D] Focus chain O [auth A] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain LA [auth D] Focus chain O [auth A] Focus chain W [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Q [auth A]	Q [auth A], Y [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain Y [auth B] Interactions & Density Focus chain Q [auth A] Focus chain Y [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain V [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain V [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], F [auth A], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], KA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.203 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.535	α = 90
b = 98.675	β = 90
c = 181.622	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394