9KBE | pdb_00009kbe

Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with indolcarboxamide

PDB DOI: https://doi.org/10.2210/pdb9KBE/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-10-30 Released: 2025-11-05
Deposition Author(s): Murakami, S., Okada, U., Yamashita, E., Pieroni, M., Carosati, E.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.242 (Depositor), 0.244 (DCC)
R-Value Work:
0.216 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with indolcarboxamide.

Murakami, S.

To be published.

Macromolecule Content

Total Structure Weight: 88.79 kDa
Atom Count: 5,866
Modeled Residue Count: 725
Deposited Residue Count: 779
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trehalose monomycolate exporter MmpL3	A	779	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: mmpL3, MSMEG_0250, MSMEI_0243
UniProt
Find proteins for A0QP27 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QP27 Go to UniProtKB: A0QP27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QP27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT (Subject of Investigation/LOI) Query on LMT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
A1L5O (Subject of Investigation/LOI) Query on A1L5O 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]	N-cycloheptyl-4,6-dimethyl-1H-indole-2-carboxamide C₁₈ H₂₄ N₂ O ANRDRZQBFPDAJD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]