7NGM

Mycobacterium tuberculosis transcriptional regulator EthR with bound inhibitory compound

PDB DOI: https://doi.org/10.2210/pdb7NGM/pdb

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

Deposited: 2021-02-09 Released: 2022-02-23
Deposition Author(s): Tomlinson, C.W.E., Tatum, N.J., Pohl, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.245
R-Value Work: 0.210
R-Value Observed: 0.212

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

Systematic exploration of the hydrophobic capacity of the EthR binding site for lead compound optimization

Tatum, N.J., Tomlinson, C.W.E., Frita, R., Bennett, R., Baulard, A.R., Pohl, E., Kitching, M.O.

To be published.

Macromolecule Content

Total Structure Weight: 24.03 kDa
Atom Count: 1,587
Modelled Residue Count: 193
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A	216	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: ethR, etaR, Rv3855
UniProt
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMC1 Go to UniProtKB: P9WMC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WMC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UAK (Subject of Investigation/LOI) Query on UAK Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-methyl-~{N}-[(1~{R})-1-phenylethyl]piperidine-1-carboxamide C₁₅ H₂₂ N₂ O PSSJJOIQPKCPGY-CYBMUJFWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.245
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.416	α = 90
b = 121.416	β = 90
c = 33.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Tomlinson, C.W.E.

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.