7TMF | pdb_00007tmf

Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (short b-axis)

PDB DOI: https://doi.org/10.2210/pdb7TMF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-19 Released: 2022-02-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.230 (Depositor), 0.229 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of NAD(P)H nitroreductases from Klebsiella pneumoniae

Kancherla, A.D., Liu, L., Tillery, L., Shek, R., Craig, J.K., Machen, A.J., Seibold, S., Battaile, K.P., Fradi, S., Barrett, L.K., Subramanian, S., Myler, P., Van Voorhis, W.C., Lovell, S.

(2024) Acta Crystallogr F Struct Biol Commun F80: 173-182

DOI: https://doi.org/10.1107/S2053230X24006472

Macromolecule Content

Total Structure Weight: 44.98 kDa
Atom Count: 3,039
Modeled Residue Count: 354
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H nitroreductase	A, B	191	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0 Gene Names: ydjA, E3U37_20475, E3U38_02825, E9161_16570, NCTC9504_03979 EC: 1
UniProt
Find proteins for A0A0H3GLR2 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GLR2 Go to UniProtKB: A0A0H3GLR2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3GLR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] N [auth B] F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B]