7NOR

Crystal structure of Mycobacterium tuberculosis ArgF in complex with 2-fluoro-4-hydroxybenzonitrile.

PDB DOI: https://doi.org/10.2210/pdb7NOR/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-25 Released: 2021-06-30
Deposition Author(s): Mendes, V., Gupta, P., Burgess, A., Sebastian-Perez, V., Cattermole, E., Meghir, C., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.186
R-Value Work: 0.167
R-Value Observed: 0.168

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis

Gupta, P., Thomas, S.E., Zaidan, S.A., Pasillas, M.A., Cory-Wright, J., Sebastian-Perez, V., Burgess, A., Cattermole, E., Meghir, C., Abell, C., Coyne, A.G., Jacobs, W.R., Blundell, T.L., Tiwari, S., Mendes, V.

(2021) Comput Struct Biotechnol J 19: 3491-3506

DOI: https://doi.org/10.1016/j.csbj.2021.06.006

Macromolecule Content

Total Structure Weight: 200.75 kDa
Atom Count: 15,246
Modelled Residue Count: 1,810
Deposited Residue Count: 1,854
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C, D, E A, B, C, D, E, F	309	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: argF, Rv1656, MTCY06H11.21 EC: 2.1.3.3
UniProt
Find proteins for P9WIT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIT9 Go to UniProtKB: P9WIT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8H8 (Subject of Investigation/LOI) Query on 8H8 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth D] SDF format, chain S [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E]	K [auth A], L [auth A], P [auth D], S [auth E]	2-fluoro-4-hydroxybenzonitrile C₇ H₄ F N O REIVHYDACHXPNH-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth D] Focus chain S [auth E] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth D] Focus chain S [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] M [auth C] G [auth A], H [auth A], I [auth A], J [auth A], M [auth C], N [auth C], O [auth D], Q [auth E], R [auth E], T [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F]