7NNC

Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal-5'-phosphate and 6-Methoxyquinoline-3-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb7NNC/pdb

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

Deposited: 2021-02-24 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: 1.70 Å
R-Value Free: 0.162
R-Value Work: 0.145
R-Value Observed: 0.146

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: 165.63 kDa
Atom Count: 12,966
Modelled Residue Count: 1,564
Deposited Residue Count: 1,608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylornithine aminotransferase	A, B, C, D	402	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: argD, Rv1655, MTCY06H11.20 EC: 2.6.1.11
UniProt
Find proteins for P9WPZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPZ7 Go to UniProtKB: P9WPZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UMH (Subject of Investigation/LOI) Query on UMH Download Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	6-methoxyquinoline-3-carboxylic acid C₁₁ H₉ N O₃ QSFFBQNKTUMKNW-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth D] MOL2 format, chain E [auth B] MOL2 format, chain G [auth D] mmCIF format, chain E [auth B] mmCIF format, chain G [auth D]	E [auth B], G [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain G [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.162
R-Value Work: 0.145
R-Value Observed: 0.146
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.461	α = 90
b = 184.944	β = 106.06
c = 71.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	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.