9HAV | pdb_00009hav

F420-dependent glucose-6-phosphate dehydrogenase from Thermomicrobium roseus with glucose

PDB DOI: https://doi.org/10.2210/pdb9HAV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermomicrobium roseum DSM 5159
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-05 Released: 2025-11-19
Deposition Author(s): Palm, G.J., Berndt, L., Lammers, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)

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

Discovery of a coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Thermomicrobium roseum

Last, D., Hasan, M., Memman, J.L., Kroeber, T.D.U., Palm, G.J., Lammers, M., Lackner, G.

To be published.

Macromolecule Content

Total Structure Weight: 255 kDa
Atom Count: 16,745
Modeled Residue Count: 2,017
Deposited Residue Count: 2,280
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferase family protein	A B C D [auth F] E A, B, C, D [auth F], E, F [auth D]	380	Thermomicrobium roseum DSM 5159	Mutation(s): 0 Gene Names: trd_A0676
UniProt
Find proteins for B9L4G2 (Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2)) Explore B9L4G2 Go to UniProtKB: B9L4G2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9L4G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth F] SDF format, chain N [auth E] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth F] MOL2 format, chain N [auth E] MOL2 format, chain O [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth F] mmCIF format, chain N [auth E] mmCIF format, chain O [auth D]	G [auth A] H [auth B] J [auth C] L [auth F] N [auth E] G [auth A], H [auth B], J [auth C], L [auth F], N [auth E], O [auth D]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth F] Focus chain N [auth E] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth F] Focus chain N [auth E] Focus chain O [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth F] SDF format, chain P [auth D] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth F] MOL2 format, chain P [auth D] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth F] mmCIF format, chain P [auth D]	I [auth B], K [auth C], M [auth F], P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth F] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth F] Focus chain P [auth D]