9HCI | pdb_00009hci

structure of the double Cys-substituted cross-linked AcrB variant S562C_T837C

PDB DOI: https://doi.org/10.2210/pdb9HCI/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli B, Escherichia coli K-12
Mutation(s): Yes

Deposited: 2024-11-10 Released: 2025-11-19
Deposition Author(s): Brandstaetter, L., Mueller, R.T., Pos, K.M.
Funding Organization(s): Swiss National Science Foundation, University of Zurich, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.230 (Depositor), 0.233 (DCC)
R-Value Work:
0.190 (Depositor), 0.197 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps.

Bornsen, C., Muller, R.T., Vieira Da Cruz, A., Jimenez-Castellanos, J.C., Meurillon, V., Brandstatter, L., Lodinsky, E.V., Athar, M., Vargiu, A.V., Hartkoorn, R.C., Flipo, M., Frangakis, A.S., Pos, K.M.

(2026) NPJ Antimicrob Resist 4

PubMed: 42082832 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44259-026-00207-6
Primary Citation Related Structures:
9HAO, 9HCI

PubMed Abstract:
In many Gram-negative bacteria such as Escherichia coli and Klebsiella pneumoniae, the AcrAB-TolC efflux pump is central to multidrug resistance. We report the development of BDM91531, a nanomolar pyridylpiperazine inhibitor that potentiates the activity of several antibiotics. Structural analyses by X-ray crystallography and cryo-EM revealed that the divalent cationic BDM91531 binds AcrB through electrostatic interactions with a central role for residues D408 and E947, trapping protomers in an O to L transitional state and blocking the conformational cycling of the trimer. Differential scanning fluorimetry and susceptibility tests confirmed this inhibitory mechanism. Negative charges at the cytoplasmic rim are essential for inhibitor uptake as electrostatic attraction from rim carboxylates, including E947 and D951, facilitates entry. Loss of D951 abolished inhibitor sensitivity, whereas introducing alternative negative charges restored activity. These findings establish BDM91531 as a potent AcrB efflux pump inhibitor and highlight structural determinants for inhibitor access and binding.

Organizational Affiliation

Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 389.33 kDa
Atom Count: 27,769
Modeled Residue Count: 3,418
Deposited Residue Count: 3,509
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,057	Escherichia coli K-12	Mutation(s): 2 Gene Names: acrB, acrE, b0462, JW0451
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224 Go to UniProtKB: P31224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain W [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B]	BA [auth B] F [auth A] G [auth A] GA [auth C] H [auth A] BA [auth B], F [auth A], G [auth A], GA [auth C], H [auth A], J [auth A], N [auth A], W [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain BA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain BA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth A] Focus chain W [auth B]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain EA [auth C]	EA [auth C]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Interactions & Density Focus chain EA [auth C]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain Y [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain Y [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain Y [auth B]	IA [auth C], L [auth A], LA [auth C], Y [auth B]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain IA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain Y [auth B]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain UA [auth C] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain TA [auth C] SDF format, chain I [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain I [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain I [auth A]	I [auth A] KA [auth C] MA [auth C] Q [auth B] S [auth B] I [auth A], KA [auth C], MA [auth C], Q [auth B], S [auth B], TA [auth C], UA [auth C], X [auth B], Z [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain Q [auth B] Focus chain S [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain Q [auth B] Focus chain S [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain X [auth B] Focus chain Z [auth B]
DD9 Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain OA [auth C] MOL2 format, chain OA [auth C] mmCIF format, chain OA [auth C]	OA [auth C]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain OA [auth C] Interactions & Density Focus chain OA [auth C]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain JA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth C]	HA [auth C], JA [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain JA [auth C] Interactions & Density Focus chain HA [auth C] Focus chain JA [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain SA [auth C] MOL2 format, chain SA [auth C] mmCIF format, chain SA [auth C]	SA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain SA [auth C] Interactions & Density Focus chain SA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth C] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain QA [auth C] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D]	CA [auth B] DA [auth B] FA [auth C] K [auth A] M [auth A] CA [auth B], DA [auth B], FA [auth C], K [auth A], M [auth A], O [auth B], P [auth B], QA [auth C], R [auth B], RA [auth C], T [auth B], U [auth B], V [auth B], VA [auth D], WA [auth D], XA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain NA [auth C] SDF format, chain PA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain PA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain NA [auth C] mmCIF format, chain PA [auth C]	AA [auth B], NA [auth C], PA [auth C]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain NA [auth C] Focus chain PA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain NA [auth C] Focus chain PA [auth C]