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 1.0 of the entry. See complete history.

Literature

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

Boernsen, C., Mueller, R.T., Pos, K.M.

To be published.

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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 I [auth A] SDF format, chain KA [auth C] SDF format, chain MA [auth C] 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 Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] 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 Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth C] 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 Q [auth B]	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 P [auth B] SDF format, chain QA [auth C] 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 XA [auth D] SDF format, chain WA [auth D] SDF format, chain R [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth C] 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 XA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth C] 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 XA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	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]