8QPO

E. coli NfsB with the unnatural amino acid p-nitrophenylalanine at position 124.

PDB DOI: https://doi.org/10.2210/pdb8QPO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli DH5[alpha]
Expression System: Escherichia coli str. K-12 substr. DH10B
Mutation(s): No

Deposited: 2023-10-02 Released: 2024-08-14
Deposition Author(s): Day, M.A., White, S.A., Hyde, E.I.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.201
R-Value Work: 0.170
R-Value Observed: 0.172

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

E. coli NfsB with unnatural amino acids at position 124.

Day, M.A., White, S.A., Searle, P.F., Hyde, E.I.

To be published.

Macromolecule Content

Total Structure Weight: 199.69 kDa
Atom Count: 14,090
Modelled Residue Count: 1,728
Deposited Residue Count: 1,768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-insensitive NAD(P)H nitroreductase	A, B, C, D, E A, B, C, D, E, F, G, H	221	Escherichia coli DH5[alpha]	Mutation(s): 0 Gene Names: nfsB, dprA, nfnB, nfsI, ntr, b0578, JW0567 EC: 1 (PDB Primary Data), 1.5.1.34 (PDB Primary Data)
UniProt
Find proteins for P38489 (Escherichia coli (strain K12)) Explore P38489 Go to UniProtKB: P38489
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain T [auth G] SDF format, chain V [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain T [auth G] MOL2 format, chain V [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain T [auth G] mmCIF format, chain V [auth H]	I [auth A] K [auth B] M [auth C] N [auth D] P [auth E] I [auth A], K [auth B], M [auth C], N [auth D], P [auth E], R [auth F], T [auth G], V [auth H]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	J [auth A] L [auth B] O [auth D] Q [auth E] S [auth F] J [auth A], L [auth B], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]