9D6X | pdb_00009d6x

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Monoclinic P form)

• PDB DOI: https://doi.org/10.2210/pdb9D6X/pdb

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


• Deposited: 2024-08-16 Released: 2025-08-20 
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Monoclinic P form)

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 153.76 kDa 
• Atom Count: 10,666 
• Modeled Residue Count: 1,313 
• Deposited Residue Count: 1,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin reductase 1	A, B, C, D	348	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTX (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], K [auth D]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N
CL	E [auth A], G [auth B], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.273	α = 90
b = 83.863	β = 90.34
c = 98.674	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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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

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release