8ZKP | pdb_00008zkp

Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C3 symmetry

PDB DOI: https://doi.org/10.2210/pdb8ZKP/pdb
EM Map EMD-60202: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv, Mycolicibacterium smegmatis MC2 155
Expression System: Mycolicibacterium smegmatis MC2 155
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2024-05-17 Released: 2025-05-21
Deposition Author(s): Zhang, B., Xiong, Z., Rao, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.64 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

membrane transporter

Zhang, B., Xiong, Z., Rao, Z.

To be published.

Macromolecule Content

Total Structure Weight: 406.82 kDa
Atom Count: 21,087
Modeled Residue Count: 2,667
Deposited Residue Count: 3,615
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Siderophore exporter MmpL5	A, D [auth B], G [auth E]	964	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: mmpL5, Rv0676c, MTV040.04c Membrane Entity: Yes
UniProt
Find proteins for P9WJV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJV1 Go to UniProtKB: P9WJV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WJV1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Siderophore export accessory protein MmpS5	B [auth F], E [auth C], H [auth G]	142	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: mmpS5, Rv0677c, MTV040.05c Membrane Entity: Yes
UniProt
Find proteins for P9WJS7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJS7 Go to UniProtKB: P9WJS7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WJS7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Meromycolate extension acyl carrier protein	C [auth H], F [auth D], I	99	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: acpM, MSMEG_4326, MSMEI_4226
UniProt
Find proteins for A0R0B3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R0B3 Go to UniProtKB: A0R0B3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R0B3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain P [auth B]	J [auth A] K [auth A] O [auth B] P [auth B] T [auth E] J [auth A], K [auth A], O [auth B], P [auth B], T [auth E], U [auth E]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth E] Focus chain U [auth E]
PEV (Subject of Investigation/LOI) Query on PEV Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain W [auth G] SDF format, chain V [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth G] MOL2 format, chain V [auth E] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth G] mmCIF format, chain V [auth E]	L [auth A] M [auth A] Q [auth B] R [auth C] V [auth E] L [auth A], M [auth A], Q [auth B], R [auth C], V [auth E], W [auth G]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₃₉ H₇₈ N O₈ P RPJZYOHZALDGKI-QNGWXLTQSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain V [auth E] Focus chain W [auth G] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain V [auth E] Focus chain W [auth G]
PN7 (Subject of Investigation/LOI) Query on PN7 Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain X [auth I] SDF format, chain N [auth H] MOL2 format, chain S [auth D] MOL2 format, chain X [auth I] MOL2 format, chain N [auth H] mmCIF format, chain S [auth D] mmCIF format, chain X [auth I] mmCIF format, chain N [auth H]	N [auth H], S [auth D], X [auth I]	N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide C₁₁ H₂₃ N₂ O₇ P S JDMUPRLRUUMCTL-SECBINFHSA-N		Interactions Focus chain N [auth H] Focus chain S [auth D] Focus chain X [auth I] Interactions & Density Focus chain N [auth H] Focus chain S [auth D] Focus chain X [auth I]