8YSW | pdb_00008ysw

phosphinothricin dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb8YSW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lysinibacillus composti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-23 Released: 2025-04-09
Deposition Author(s): Xue, Y.P., Cheng, F., Zhou, S.P., Xu, J.M., Jin, L.Q., Ma, C.J., Zheng, Y.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.192 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (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

Crystal Structure of phosphinothricin dehydrogenase with NAD at 2.6 Angstorms resolution

Xue, Y.P., Cheng, F., Zhou, S.P., Xu, J.M., Jin, L.Q., Zheng, Y.G.

To be published.

Macromolecule Content

Total Structure Weight: 278.91 kDa
Atom Count: 18,918
Modeled Residue Count: 2,362
Deposited Residue Count: 2,490
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E A, B, C, D, E, F	415	Lysinibacillus composti	Mutation(s): 0 Gene Names: EBB45_13425
UniProt
Find proteins for A0A3N9UCW8 (Lysinibacillus composti) Explore A0A3N9UCW8 Go to UniProtKB: A0A3N9UCW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3N9UCW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth B], O [auth C], Q [auth E], T [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth E] Focus chain T [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain R [auth F] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth F] MOL2 format, chain R [auth F] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth F] mmCIF format, chain R [auth F] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], P [auth D], R [auth F], S [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth F] Focus chain S [auth F]