6ZO6

Minocycline binding to the deep binding pocket of AcrB-G619P

PDB DOI: https://doi.org/10.2210/pdb6ZO6/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2020-07-07 Released: 2021-05-19
Deposition Author(s): Tam, H.K., Foong, W.E., Pos, K.M.
Funding Organization(s): German Research Foundation (DFG), German-Israeli Foundation for Research and Development, European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.257
R-Value Work: 0.231
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Allosteric drug transport mechanism of multidrug transporter AcrB.

Tam, H.K., Foong, W.E., Oswald, C., Herrmann, A., Zeng, H., Pos, K.M.

(2021) Nat Commun 12: 3889-3889

PubMed: 34188038 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-24151-3
Primary Citation of Related Structures:
6ZO5, 6ZO6, 6ZO7, 6ZO8, 6ZO9, 6ZOA, 6ZOB, 6ZOC, 6ZOD, 6ZOE, 6ZOF, 6ZOG, 6ZOH

PubMed Abstract:
Gram-negative bacteria maintain an intrinsic resistance mechanism against entry of noxious compounds by utilizing highly efficient efflux pumps. The E. coli AcrAB-TolC drug efflux pump contains the inner membrane H ⁺/drug antiporter AcrB comprising three functionally interdependent protomers, cycling consecutively through the loose (L), tight (T) and open (O) state during cooperative catalysis. Here, we present 13 X-ray structures of AcrB in intermediate states of the transport cycle. Structure-based mutational analysis combined with drug susceptibility assays indicate that drugs are guided through dedicated transport channels toward the drug binding pockets. A co-structure obtained in the combined presence of erythromycin, linezolid, oxacillin and fusidic acid shows binding of fusidic acid deeply inside the T protomer transmembrane domain. Thiol cross-link substrate protection assays indicate that this transmembrane domain-binding site can also accommodate oxacillin or novobiocin but not erythromycin or linezolid. AcrB-mediated drug transport is suggested to be allosterically modulated in presence of multiple drugs.

Organizational Affiliation

Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany. tamhk60@hotmail.com.

Macromolecule Content

Total Structure Weight: 393.98 kDa
Atom Count: 28,139
Modelled Residue Count: 3,419
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): 1 Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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

Small Molecules

Ligands 21 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain FB [auth C] MOL2 format, chain FB [auth C]	FB [auth C]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain FB [auth C] Interactions & Density Focus chain FB [auth C]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain EB [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain F [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain F [auth A]	EB [auth C] F [auth A] G [auth A] H [auth A] X [auth B] EB [auth C], F [auth A], G [auth A], H [auth A], X [auth B], Y [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain EB [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EB [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Focus chain Y [auth B]
MIY (Subject of Investigation/LOI) Query on MIY Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B]	W [auth B]	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE C₂₃ H₂₇ N₃ O₇ DYKFCLLONBREIL-KVUCHLLUSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
LPX Query on LPX Download Ideal Coordinates CCD File SDF format, chain VB [auth C] MOL2 format, chain VB [auth C]	VB [auth C]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate C₂₁ H₄₄ N O₇ P YVYMBNSKXOXSKW-FQEVSTJZSA-N		Interactions Focus chain VB [auth C] Interactions & Density Focus chain VB [auth C]
DDR Query on DDR Download Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B]	Z [auth B]	(2S)-3-hydroxypropane-1,2-diyl didecanoate C₂₃ H₄₄ O₅ GNSDEDOVXZDMKM-NRFANRHFSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
8K6 Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain AB [auth B] MOL2 format, chain AB [auth B]	AB [auth B]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Interactions & Density Focus chain AB [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain WB [auth C] MOL2 format, chain WB [auth C]	WB [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain WB [auth C] Interactions & Density Focus chain WB [auth C]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain BB [auth B] MOL2 format, chain BB [auth B]	BB [auth B]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain BB [auth B] Interactions & Density Focus chain BB [auth B]
MYS Query on MYS Download Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B]	NA [auth B], OA [auth B]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Focus chain OA [auth B] Interactions & Density Focus chain NA [auth B] Focus chain OA [auth B]
DDQ Query on DDQ Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth B] SDF format, chain IB [auth C] SDF format, chain JB [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C]	AA [auth B], BA [auth B], IB [auth C], J [auth A], JB [auth C]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₂ H₂₇ N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JB [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JB [auth C]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain DB [auth C] MOL2 format, chain DB [auth C]	DB [auth C]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain DB [auth C] Interactions & Density Focus chain DB [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain PA [auth B] MOL2 format, chain PA [auth B]	PA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain PA [auth B] Interactions & Density Focus chain PA [auth B]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain RB [auth C] SDF format, chain Q [auth A] SDF format, chain SB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain SB [auth C]	Q [auth A], RB [auth C], SB [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain RB [auth C] Focus chain SB [auth C] Interactions & Density Focus chain Q [auth A] Focus chain RB [auth C] Focus chain SB [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain FC [auth C] SDF format, chain V [auth A] MOL2 format, chain FC [auth C] MOL2 format, chain V [auth A]	FC [auth C], V [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FC [auth C] Focus chain V [auth A] Interactions & Density Focus chain FC [auth C] Focus chain V [auth A]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain KB [auth C] SDF format, chain LB [auth C] SDF format, chain CA [auth B] SDF format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B]	CA [auth B], DA [auth B], EA [auth B], KB [auth C], LB [auth C]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain KB [auth C] Focus chain LB [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain KB [auth C] Focus chain LB [auth C]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain GB [auth C] SDF format, chain I [auth A] SDF format, chain HB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth C]	GB [auth C], HB [auth C], I [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain GB [auth C] Focus chain HB [auth C] Focus chain I [auth A] Interactions & Density Focus chain GB [auth C] Focus chain HB [auth C] Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CB [auth B] MOL2 format, chain CB [auth B]	CB [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CB [auth B] Interactions & Density Focus chain CB [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MB [auth C] SDF format, chain N [auth A] SDF format, chain NB [auth C] SDF format, chain OB [auth C] SDF format, chain P [auth A] SDF format, chain FA [auth B] SDF format, chain JC [auth E] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain OB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain JC [auth E] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A]	FA [auth B] GA [auth B] HA [auth B] IA [auth B] JC [auth E] FA [auth B], GA [auth B], HA [auth B], IA [auth B], JC [auth E], K [auth A], L [auth A], M [auth A], MB [auth C], N [auth A], NB [auth C], O [auth A], OB [auth C], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JC [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OB [auth C] Focus chain P [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JC [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OB [auth C] Focus chain P [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain R [auth A] SDF format, chain TB [auth C] SDF format, chain UB [auth C] SDF format, chain KA [auth B] SDF format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B]	KA [auth B] LA [auth B] MA [auth B] R [auth A] TB [auth C] KA [auth B], LA [auth B], MA [auth B], R [auth A], TB [auth C], UB [auth C]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain R [auth A] Focus chain TB [auth C] Focus chain UB [auth C] Interactions & Density Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain R [auth A] Focus chain TB [auth C] Focus chain UB [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BC [auth C] SDF format, chain CC [auth C] SDF format, chain DC [auth C] SDF format, chain GC [auth D] SDF format, chain HC [auth D] SDF format, chain IC [auth D] SDF format, chain QA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain YB [auth C] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] SDF format, chain AC [auth C] SDF format, chain EC [auth C] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain UA [auth B] SDF format, chain YA [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain CC [auth C] MOL2 format, chain DC [auth C] MOL2 format, chain GC [auth D] MOL2 format, chain HC [auth D] MOL2 format, chain IC [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain YB [auth C] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C] MOL2 format, chain AC [auth C] MOL2 format, chain EC [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain YA [auth B]	AC [auth C] BC [auth C] CC [auth C] DC [auth C] EC [auth C] AC [auth C], BC [auth C], CC [auth C], DC [auth C], EC [auth C], GC [auth D], HC [auth D], IC [auth D], QA [auth B], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], VA [auth B], WA [auth B], XA [auth B], XB [auth C], YA [auth B], YB [auth C], ZA [auth B], ZB [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth C] Focus chain BC [auth C] Focus chain CC [auth C] Focus chain DC [auth C] Focus chain EC [auth C] Focus chain GC [auth D] Focus chain HC [auth D] Focus chain IC [auth D] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain ZA [auth B] Focus chain ZB [auth C] Interactions & Density Focus chain AC [auth C] Focus chain BC [auth C] Focus chain CC [auth C] Focus chain DC [auth C] Focus chain EC [auth C] Focus chain GC [auth D] Focus chain HC [auth D] Focus chain IC [auth D] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain ZA [auth B] Focus chain ZB [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain QB [auth C] SDF format, chain PB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain PB [auth C]	JA [auth B], PB [auth C], QB [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth B] Focus chain PB [auth C] Focus chain QB [auth C] Interactions & Density Focus chain JA [auth B] Focus chain PB [auth C] Focus chain QB [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.257
R-Value Work: 0.231
R-Value Observed: 0.232
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.281	α = 90
b = 161.008	β = 90
c = 245.457	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Tam, H.K.

Foong, W.E.

Pos, K.M.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG-EXC115
German-Israeli Foundation for Research and Development	Germany	I-1202-248.9/2012
European Communitys Seventh Framework Programme	European Union	FP7/2007-2013

Revision History (Full details and data files)

Version 1.0: 2021-05-19
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references
Version 1.2: 2021-07-14
Changes: Database references
Version 1.3: 2024-01-31
Changes: Data collection, Database references, Refinement description