6ZO8

Minocycline binding to the deep binding pocket of AcrB-G621P

PDB DOI: https://doi.org/10.2210/pdb6ZO8/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 PDBTMMemProtMDmpstruc

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: 2.50 Å
R-Value Free: 0.249
R-Value Work: 0.219
R-Value Observed: 0.221

Starting Model: experimental
View more details

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: 394.57 kDa
Atom Count: 27,356
Modelled Residue Count: 3,421
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 17 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain RA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain RA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain RA [auth C]	RA [auth C], U [auth B]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain RA [auth C] Focus chain U [auth B] Interactions & Density Focus chain RA [auth C] Focus chain U [auth B]
LMU Query on LMU Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	DODECYL-ALPHA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-YHBSTRCHSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain OA [auth C] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain T [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], OA [auth C], PA [auth C], QA [auth C], T [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain T [auth B]
MIY (Subject of Investigation/LOI) Query on MIY Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [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 R [auth B] Interactions & Density Focus chain R [auth B]
LPX Query on LPX Download Ideal Coordinates CCD File SDF format, chain JB [auth C] SDF format, chain KB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth C]	JB [auth C], KB [auth C]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate C₂₁ H₄₄ N O₇ P YVYMBNSKXOXSKW-FQEVSTJZSA-N		Interactions Focus chain JB [auth C] Focus chain KB [auth C] Interactions & Density Focus chain JB [auth C] Focus chain KB [auth C]
DDR Query on DDR Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	(2S)-3-hydroxypropane-1,2-diyl didecanoate C₂₃ H₄₄ O₅ GNSDEDOVXZDMKM-NRFANRHFSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
DDQ Query on DDQ Download Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B] mmCIF format, chain LA [auth B]	LA [auth B]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₂ H₂₇ N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain GB [auth C] MOL2 format, chain O [auth A] MOL2 format, chain GB [auth C] mmCIF format, chain O [auth A] mmCIF format, chain GB [auth C]	GB [auth C], O [auth A]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain GB [auth C] Focus chain O [auth A] Interactions & Density Focus chain GB [auth C] Focus chain O [auth A]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain EA [auth B] SDF format, chain IB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain IB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain IB [auth C]	EA [auth B], HB [auth C], IB [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain HB [auth C] Focus chain IB [auth C] Interactions & Density Focus chain EA [auth B] Focus chain HB [auth C] Focus chain IB [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C]	BA [auth B] BB [auth C] CA [auth B] CB [auth C] DB [auth C] BA [auth B], BB [auth C], CA [auth B], CB [auth C], DB [auth C], M [auth A], N [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain M [auth A] Focus chain N [auth A]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EB [auth C] SDF format, chain FB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C]	DA [auth B], EB [auth C], FB [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EB [auth C] Focus chain FB [auth C] Interactions & Density Focus chain DA [auth B] Focus chain EB [auth C] Focus chain FB [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain QB [auth C] SDF format, chain KA [auth B] SDF format, chain PB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain PB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain PB [auth C]	KA [auth B], PB [auth C], QB [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain KA [auth B] Focus chain PB [auth C] Focus chain QB [auth C] Interactions & Density Focus chain KA [auth B] Focus chain PB [auth C] Focus chain QB [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain TA [auth C] SDF format, chain W [auth B] SDF format, chain YA [auth C] SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain SA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C]	AA [auth B] AB [auth C] K [auth A] L [auth A] SA [auth C] AA [auth B], AB [auth C], K [auth A], L [auth A], SA [auth C], TA [auth C], UA [auth C], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain LB [auth C] SDF format, chain MB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MB [auth C]	FA [auth B], LB [auth C], MB [auth C]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain LB [auth C] Focus chain MB [auth C] Interactions & Density Focus chain FA [auth B] Focus chain LB [auth C] Focus chain MB [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain JA [auth B] SDF format, chain NB [auth C] SDF format, chain RB [auth D] SDF format, chain SB [auth D] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain OB [auth C] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain TB [auth D] SDF format, chain UB [auth E] MOL2 format, chain GA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain SB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain UB [auth E] mmCIF format, chain GA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain RB [auth D] mmCIF format, chain SB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain TB [auth D] mmCIF format, chain UB [auth E]	GA [auth B] HA [auth B] IA [auth B] JA [auth B] NB [auth C] GA [auth B], HA [auth B], IA [auth B], JA [auth B], NB [auth C], OB [auth C], P [auth A], Q [auth A], RB [auth D], SB [auth D], TB [auth D], UB [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RB [auth D] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain UB [auth E] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RB [auth D] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain UB [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain NA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain NA [auth B]	NA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain NA [auth B] Interactions & Density Focus chain NA [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain MA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain MA [auth B]	MA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Interactions & Density Focus chain MA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.249
R-Value Work: 0.219
R-Value Observed: 0.221
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.414	α = 90
b = 161.617	β = 90
c = 245.041	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