7NPJ

Crystal structure of Mycobacterium tuberculosis ArgC in complex with 6-phenoxy-3-pyridinamine

PDB DOI: https://doi.org/10.2210/pdb7NPJ/pdb

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

Deposited: 2021-02-27 Released: 2021-06-30
Deposition Author(s): Gupta, P., Mendes, V., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.325
R-Value Work: 0.237
R-Value Observed: 0.242

Starting Models: 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: 292.07 kDa
Atom Count: 18,617
Modelled Residue Count: 2,752
Deposited Residue Count: 2,832
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-gamma-glutamyl-phosphate reductase	A, B, C, D, E A, B, C, D, E, F, G, H	354	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: argC, Rv1652, MTCY06H11.17 EC: 1.2.1.38
UniProt
Find proteins for P9WPZ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPZ9 Go to UniProtKB: P9WPZ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UKK (Subject of Investigation/LOI) Query on UKK Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	6-phenoxy-3-pyridinamine C₁₁ H₁₀ N₂ O DETKIRMPBJPJRQ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.325
R-Value Work: 0.237
R-Value Observed: 0.242
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.34	α = 90
b = 132.813	β = 90.12
c = 122.819	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
xia2	data reduction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1158806

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.