9GJY | pdb_00009gjy

Bacillus licheniformis nitroreductase

PDB DOI: https://doi.org/10.2210/pdb9GJY/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: 1.62 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (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: 175.95 kDa
Atom Count: 12,803
Modeled Residue Count: 1,380
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain JA [auth F] SDF format, chain V [auth C] SDF format, chain O [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain O [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain O [auth B]	AA [auth D] CA [auth E] G [auth A] JA [auth F] O [auth B] AA [auth D], CA [auth E], G [auth A], JA [auth F], O [auth B], V [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain G [auth A] Focus chain JA [auth F] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain G [auth A] Focus chain JA [auth F] Focus chain O [auth B] Focus chain V [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain LA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain LA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain LA [auth F]	DA [auth E], LA [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain LA [auth F] Interactions & Density Focus chain DA [auth E] Focus chain LA [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain H [auth A] SDF format, chain BA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth D]	BA [auth D], H [auth A], P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain BA [auth D] Focus chain H [auth A] Focus chain P [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain N [auth B] SDF format, chain KA [auth F] SDF format, chain IA [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain N [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain IA [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain N [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain IA [auth F]	FA [auth E] IA [auth F] KA [auth F] N [auth B] W [auth C] FA [auth E], IA [auth F], KA [auth F], N [auth B], W [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain IA [auth F] Focus chain KA [auth F] Focus chain N [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain IA [auth F] Focus chain KA [auth F] Focus chain N [auth B] Focus chain W [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain U [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth E]	EA [auth E] I [auth A] J [auth A] K [auth A] M [auth A] EA [auth E], I [auth A], J [auth A], K [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], U [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Interactions & Density Focus chain EA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain L [auth A] SDF format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain L [auth A] MOL2 format, chain GA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain L [auth A] mmCIF format, chain GA [auth E]	GA [auth E], HA [auth F], L [auth A], X [auth C], Y [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain GA [auth E] Focus chain HA [auth F] Focus chain L [auth A] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth E] Focus chain HA [auth F] Focus chain L [auth A] Focus chain X [auth C] Focus chain Y [auth C]