8K1P | pdb_00008k1p

mycobacterial efflux pump, ADP+vanadate bound state

PDB DOI: https://doi.org/10.2210/pdb8K1P/pdb
EM Map EMD-36798: EMDB EMDataResource

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

Deposited: 2023-07-11 Released: 2024-07-17
Deposition Author(s): Wang, Y., Wu, F., Zhang, L., Rao, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

mycobacterial efflux pump, ADP+vanadate bound state

Wang, Y., Wu, F., Zhang, L., Rao, Z.

To be published.

Macromolecule Content

Total Structure Weight: 127.71 kDa
Atom Count: 7,139
Modeled Residue Count: 934
Deposited Residue Count: 1,170
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux system permease protein Rv1217c	A	548	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv1217c Membrane Entity: Yes
UniProt
Find proteins for O05318 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O05318 Go to UniProtKB: O05318
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O05318
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux system ATP-binding protein Rv1218c	B, C	311	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv1218c EC: 7.6.2 Membrane Entity: Yes
UniProt
Find proteins for O86311 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O86311 Go to UniProtKB: O86311
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O86311
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
VO4 Query on VO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	VANADATE ION O₄ V LSGOVYNHVSXFFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B]	F [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth C] Interactions & Density Focus chain F [auth B] Focus chain I [auth C]