9KSN | pdb_00009ksn

Crystal structure of meso-diaminopimelate dehydrogenase from Bacillus thermozeamaize mutant M9 complexed with NADP+

PDB DOI: https://doi.org/10.2210/pdb9KSN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus thermozeamaize
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-30 Released: 2025-05-21
Deposition Author(s): Wei, Y., Geng, Q., Zheng, Y.-C., Zhang, Z.-J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.201 (Depositor), 0.204 (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

An Engineered meso-Diaminopimelate Dehydrogenase Enables the Biocatalytic Synthesis of Bulky beta-Substituted d-Amino Acids

Wei, Y., Zheng, Y.C., Liu, H.P., Geng, Q., Wang, Z., Wang, Y.Q., Yu, H.L., Xu, J.H., Zhang, Z.J.

(2025) ACS Catal : 7720-7730

DOI: https://doi.org/10.1021/acscatal.5c01214

Macromolecule Content

Total Structure Weight: 117.68 kDa
Atom Count: 7,313
Modeled Residue Count: 914
Deposited Residue Count: 1,041
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meso-diaminopimelate D-dehydrogenase	A, B, C	347	Bacillus thermozeamaize	Mutation(s): 0 Gene Names: BAA01_00405 EC: 1.4.1.16
UniProt
Find proteins for A0A1Y3PXT7 (Bacillus thermozeamaize) Explore A0A1Y3PXT7 Go to UniProtKB: A0A1Y3PXT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y3PXT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 O [auth C] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain O [auth C] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain O [auth C] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], O [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain O [auth C]
OXM Query on OXM Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], P [auth C], Q [auth C]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain Q [auth C]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A] J [auth B] K [auth B] L [auth B] N [auth B] F [auth A], J [auth B], K [auth B], L [auth B], N [auth B], R [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain R [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]