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 PDBTM MemProtMD

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

Validation slider image for 8K1P

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05318
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32170703

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release
Version 1.1: 2025-07-02
Changes: Data collection, Structure summary

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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.