9NEJ | pdb_00009nej

AZD-3 bound EFPA transporter of Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb9NEJ/pdb
EM Map EMD-49313: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2025-02-19 Released: 2026-03-04
Deposition Author(s): Khandelwal, N.K., Gupta, M., Stroud, R.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NEJ

This is version 1.0 of the entry. See complete history.

Literature

AZD-3 bound EFPA transporter of Mycobacterium tuberculosis

Khandelwal, N.K., Gupta, M., Stroud, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 138.35 kDa
Atom Count: 7,208
Modeled Residue Count: 940
Deposited Residue Count: 1,258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized MFS-type transporter EfpA	A, B	629	Mycobacterium tuberculosis H37Rv	Mutation(s): 1 Gene Names: efpA, Rv2846c
UniProt
Find proteins for P9WJY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJY5 Go to UniProtKB: P9WJY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJY5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BXT Query on A1BXT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(2R)-3-{[(S)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(10E)-hexadec-10-enoyl]oxy}propyl (9E,14E)-octadeca-9,14-dienoate C₄₀ H₇₃ O₁₀ P UAKNDDGOSJFMJQ-JMBLMXHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
A1ATG (Subject of Investigation/LOI) Query on A1ATG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], F [auth B], H [auth B], I [auth B], J [auth B]	(2S)-3-{[(R)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(2E,9E,13E)-hexadeca-2,9,13-trienoyl]oxy}propyl (4E,9E,11Z,15E)-octadeca-4,9,11,15-tetraenoate C₄₀ H₆₅ O₁₀ P QWNODTQZPQWNIK-WKOXGUCKSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
A1BXW (Subject of Investigation/LOI) Query on A1BXW Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	(2P)-2-(2-methoxyphenyl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrrolo[3,2-c]pyridin-4-amine C₂₂ H₂₁ N₃ O₂ UQASDSGYXMMHAO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.2.1
MODEL REFINEMENT	PHENIX	1.21_5207-000

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Khandelwal, N.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM024485

Revision History (Full details and data files)

Version 1.0: 2026-03-04
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.