9GJX | pdb_00009gjx

Bacillus licheniformis nitroreductase

PDB DOI: https://doi.org/10.2210/pdb9GJX/pdb

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

Deposited: 2024-08-23 Released: 2025-09-03
Deposition Author(s): Crennell, S.J., Danson, M.J., Emptage, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.164 (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

Structure of Bacillus licheniformis nitroreductase and analysis of prodrug specificity

Crennell, S.J., Danson, M.J., Emptage, C., Nesbitt, E., Porter, M.

To be published.

Macromolecule Content

Total Structure Weight: 177.97 kDa
Atom Count: 12,023
Modeled Residue Count: 1,366
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent nitro/flavin oxidoreductase	A, B, C, D, E A, B, C, D, E, F	248	Bacillus licheniformis	Mutation(s): 0 Gene Names: nfsB, BL03079
UniProt
Find proteins for Q65MG6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65MG6 Go to UniProtKB: Q65MG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q65MG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain YA [auth F] SDF format, chain R [auth B] SDF format, chain PA [auth E] SDF format, chain IA [auth D] SDF format, chain G [auth A] SDF format, chain AA [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain IA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain IA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth C]	AA [auth C] G [auth A] IA [auth D] PA [auth E] R [auth B] AA [auth C], G [auth A], IA [auth D], PA [auth E], R [auth B], YA [auth F]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain IA [auth D] Focus chain PA [auth E] Focus chain R [auth B] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain IA [auth D] Focus chain PA [auth E] Focus chain R [auth B] Focus chain YA [auth F]
CB1 Query on CB1 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain VA [auth E] SDF format, chain Q [auth B] SDF format, chain HA [auth D] SDF format, chain DA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain VA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain DA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain VA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain DA [auth C]	DA [auth C], HA [auth D], L [auth A], Q [auth B], VA [auth E]	5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE C₉ H₈ N₄ O₅ WOCXQMCIOTUMJV-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain Q [auth B] Focus chain VA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain Q [auth B] Focus chain VA [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain TA [auth E] SDF format, chain KA [auth D] SDF format, chain J [auth A] MOL2 format, chain X [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain KA [auth D] MOL2 format, chain J [auth A] mmCIF format, chain X [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain KA [auth D] mmCIF format, chain J [auth A]	J [auth A], KA [auth D], TA [auth E], X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain KA [auth D] Focus chain TA [auth E] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain KA [auth D] Focus chain TA [auth E] Focus chain X [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain FA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain FA [auth C]	FA [auth C], O [auth A], OA [auth D], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth C] Focus chain O [auth A] Focus chain OA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain O [auth A] Focus chain OA [auth D] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain UA [auth E] SDF format, chain T [auth B] SDF format, chain RA [auth E] SDF format, chain QA [auth E] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain CA [auth C] MOL2 format, chain UA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain UA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain CA [auth C]	CA [auth C] GA [auth D] H [auth A] K [auth A] P [auth B] CA [auth C], GA [auth D], H [auth A], K [auth A], P [auth B], QA [auth E], RA [auth E], T [auth B], UA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain T [auth B] Focus chain UA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain T [auth B] Focus chain UA [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain Y [auth B] SDF format, chain XA [auth F] SDF format, chain WA [auth E] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain SA [auth E] SDF format, chain S [auth B] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain JA [auth D] SDF format, chain I [auth A] SDF format, chain EA [auth C] SDF format, chain BB [auth F] SDF format, chain BA [auth C] SDF format, chain AB [auth F] MOL2 format, chain ZA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth F] mmCIF format, chain ZA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth F]	AB [auth F] BA [auth C] BB [auth F] EA [auth C] I [auth A] AB [auth F], BA [auth C], BB [auth F], EA [auth C], I [auth A], JA [auth D], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], S [auth B], SA [auth E], U [auth B], V [auth B], W [auth B], WA [auth E], XA [auth F], Y [auth B], ZA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain EA [auth C] Focus chain I [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth E] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain EA [auth C] Focus chain I [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth E] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain ZA [auth F]