9B2F | pdb_00009b2f

Crystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NAD+

• PDB DOI: https://doi.org/10.2210/pdb9B2F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-15 Released: 2025-03-19 
• Deposition Author(s): Pakhomova, S., Belyaeva, O.V., Boeglin, W.E., Kedishvili, N.Y., Brash, A.R., Newcomer, M.E., Popov, K.M.
• Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.193 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.179 (DCC) 

Starting Model: experimental

Literature

The large substrate binding pocket of dehydrogenase reductase 9 underlies its ability to oxidize diverse pro-inflammatory and pro-resolving oxylipins.

Pakhomova, S., Belyaeva, O.V., Boeglin, W.E., Kedishvili, N.Y., Brash, A.R., Newcomer, M.E., Popov, K.M.

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

Macromolecule Content 

• Total Structure Weight: 36.05 kDa 
• Atom Count: 2,537 
• Modeled Residue Count: 299 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase/reductase SDR family member 9	A	319	Mus musculus	Mutation(s): 0  Gene Names: Dhrs9 EC: 1.1.1.209 (PDB Primary Data), 1.1.1.53 (PDB Primary Data), 1.1.1.105 (PDB Primary Data)
UniProt
Find proteins for Q58NB6 (Mus musculus) Explore Q58NB6  Go to UniProtKB:  Q58NB6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MLI	C [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.193 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.179 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.384	α = 90
b = 103.045	β = 90
c = 103.082	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Pakhomova, S., Belyaeva, O.V., Boeglin, W.E., Kedishvili, N.Y., Brash, A.R., Newcomer, M.E., Popov, K.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	AR076924
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM134548

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release