9JMX | pdb_00009jmx

Crystal structure of IRED-M235A in complex with NADP+ and substrate

• PDB DOI: https://doi.org/10.2210/pdb9JMX/pdb

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


• Deposited: 2024-09-21 Released: 2025-07-23 
• Deposition Author(s): Fu, X.L., Zhang, M.T., Yi, S.M., Dai, K.X., Yang, Y.Y., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.260 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: in silico

Literature

Mutagenesis of a Single Site Inverts the Stereopreference of Imine Reductase

Li, Y., Yang, Y., Zhang, M., Yue, X., Guo, R.T., Huang, Z., Chen, F.

(2025) ACS Catal 15: 2192-2199

• DOI: https://doi.org/10.1021/acscatal.5c00046

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)

Macromolecule Content 

• Total Structure Weight: 62.21 kDa 
• Atom Count: 4,515 
• Modeled Residue Count: 567 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase	A, B	286	Amycolatopsis thermoflava	Mutation(s): 1  Gene Names: EDD35_0917
UniProt
Find proteins for A0A3N2GPT5 (Amycolatopsis thermoflava) Explore A0A3N2GPT5  Go to UniProtKB:  A0A3N2GPT5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
A1ECB (Subject of Investigation/LOI)	D [auth A], F [auth B]	1-~{tert}-butyl-4,9-dihydro-3~{H}-pyrido[3,4-b]indole C15 H18 N2 DVKOBRNFRYPBPD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.260 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.753	α = 90
b = 78.753	β = 90
c = 160.405	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
SAINT	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Fu, X.L., Zhang, M.T., Yi, S.M., Dai, K.X., Yang, Y.Y., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA0911400

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Database references