9JMY | pdb_00009jmy

Crystal structure of IRED in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb9JMY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amycolatopsis thermoflava
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-22 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.243 (Depositor), 0.247 (DCC)
R-Value Work:
0.174 (Depositor), 0.183 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 62.37 kDa
Atom Count: 4,519
Modeled Residue Count: 568
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase	A, B	286	Amycolatopsis thermoflava	Mutation(s): 0 Gene Names: EDD35_0917
UniProt
Find proteins for A0A3N2GPT5 (Amycolatopsis thermoflava) Explore A0A3N2GPT5 Go to UniProtKB: A0A3N2GPT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3N2GPT5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B]	H [auth A], I [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]