8ZXS | pdb_00008zxs

Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8ZXS/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2024-06-15 Released: 2025-06-18
Deposition Author(s): Murakami, S., Yamashita, E., Okada, U.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.288 (Depositor), 0.290 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (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 multidrug efflux transporter OqxB from Klebsiella pneumoniae

Murakami, S., Yamashita, E., Okada, U.

To be published.

Macromolecule Content

Total Structure Weight: 346.34 kDa
Atom Count: 23,984
Modeled Residue Count: 3,123
Deposited Residue Count: 3,168
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Efflux pump membrane transporter	A, B, C	1,056	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bepE_2, bepE_1, B5L96_27435, GJJ13_005705, GJJ18_08150, NCTC204_03625, NCTC9637_01899, QIG75_20820, SAMEA4364603_03846 Membrane Entity: Yes
UniProt
Find proteins for U5U6L7 (Klebsiella pneumoniae) Explore U5U6L7 Go to UniProtKB: U5U6L7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5U6L7
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 D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.288 (Depositor), 0.290 (DCC)
R-Value Work: 0.236 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.392	α = 90
b = 165.939	β = 90
c = 249.032	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Murakami, S.

Yamashita, E.

Okada, U.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H02412
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K06079
Japan Society for the Promotion of Science (JSPS)	Japan	21K19337