9HAY | pdb_00009hay

F420-dependent glucose-6-phosphate dehydrogenase with glucose-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb9HAY/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: 2.39 Å
R-Value Free:
0.191 (Depositor), 0.189 (DCC)
R-Value Work:
0.173 (Depositor), 0.172 (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., Hemmann, J.T., Kroeber, T.D.U., Palm, G.J., Lammers, M., Lackner, G.

To be published.

Macromolecule Content

Total Structure Weight: 766.79 kDa
Atom Count: 50,579
Modeled Residue Count: 6,081
Deposited Residue Count: 6,840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferase family protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9L4G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BG6 (Subject of Investigation/LOI) Query on BG6 Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain BA [auth J] SDF format, chain DA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth M] SDF format, chain HA [auth N] SDF format, chain JA [auth O] SDF format, chain LA [auth P] SDF format, chain MA [auth Q] SDF format, chain OA [auth R] SDF format, chain S [auth A] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain V [auth D] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain DA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth N] MOL2 format, chain JA [auth O] MOL2 format, chain LA [auth P] MOL2 format, chain MA [auth Q] MOL2 format, chain OA [auth R] MOL2 format, chain S [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain AA [auth I] mmCIF format, chain BA [auth J] mmCIF format, chain DA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth N] mmCIF format, chain JA [auth O] mmCIF format, chain LA [auth P] mmCIF format, chain MA [auth Q] mmCIF format, chain OA [auth R] mmCIF format, chain S [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth H]	AA [auth I] BA [auth J] DA [auth K] FA [auth L] GA [auth M] AA [auth I], BA [auth J], DA [auth K], FA [auth L], GA [auth M], HA [auth N], JA [auth O], LA [auth P], MA [auth Q], OA [auth R], S [auth A], T [auth B], U [auth C], V [auth D], W [auth E], X [auth F], Y [auth G], Z [auth H]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain JA [auth O] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain OA [auth R] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain JA [auth O] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain OA [auth R] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth H]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth K] MOL2 format, chain EA [auth K] mmCIF format, chain EA [auth K]	EA [auth K]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain EA [auth K] Interactions & Density Focus chain EA [auth K]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain KA [auth O] MOL2 format, chain KA [auth O] mmCIF format, chain KA [auth O]	KA [auth O]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain KA [auth O] Interactions & Density Focus chain KA [auth O]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain IA [auth N] MOL2 format, chain CA [auth J] MOL2 format, chain IA [auth N] mmCIF format, chain CA [auth J] mmCIF format, chain IA [auth N]	CA [auth J], IA [auth N]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Focus chain IA [auth N] Interactions & Density Focus chain CA [auth J] Focus chain IA [auth N]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain NA [auth Q] MOL2 format, chain NA [auth Q] mmCIF format, chain NA [auth Q]	NA [auth Q]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain NA [auth Q] Interactions & Density Focus chain NA [auth Q]