6zo6

Minocycline binding to the deep binding pocket of AcrB-G619P

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Multidrug efflux pump subunit AcrB

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	DARPIN × 2 DODECYL-BETA-D-MALTOSIDE × 6 N-OCTANE × 3 DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 5 GLYCEROL × 14 DODECANE × 3 HEXANE × 6 1,2-ETHANEDIOL × 24 TRIETHYLENE GLYCOL × 2 (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 × 1 (2S)-3-hydroxypropane-1,2-diyl didecanoate × 1 DECANE × 5 CHLORIDE ION × 3 PENTADECANE × 2 TETRAETHYLENE GLYCOL × 1 Octadecane × 1 HEXADECANE × 1 SULFATE ION × 1 TETRADECANE × 1 PHOSPHATIDYLETHANOLAMINE × 1 (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate × 1 PENTAETHYLENE GLYCOL × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACRB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1049； UniProt 1–1049 Author chain B； PDBConstruct 1–1049； UniProt 1–1049 Author chain C； PDBConstruct 1–1049； UniProt 1–1049

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6zo6
Deposition date deposition_date	2020-07-07
Structure title title	Minocycline binding to the deep binding pocket of AcrB-G619P
Keywords keywords	Multidrug efflux pump, Membrane protein, Transport protein; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6zo6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6zo6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zo6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	47.88 Å
Rg (electron density)	47.25 Å
Total Rg	47.49 Å
Atom count	26866
Residues	3419
Excluded volume	488560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zo6__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (24)

Entity 1 Entity 1 polymer

Description description	Multidrug efflux pump subunit AcrB
Molecular weight formula_weight	114776.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	28139

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAPRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHHLEHHHHHH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DARPIN
Molecular weight formula_weight	18317.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

MRGSHHHHHHGSDLGKKLLEAARAGRDDEVRILMANGADVNAADVVGWTPLHLAAYWGHLEIVEVLLKNGADVNAYDTLGSTPLHLAAHFGHLEIVEVLLKNGADVNAKDDNGITPLHLAANRGHLEIVEVLLKYGADVNAQDKFGKTAFDISINNGNEDLAEILQKLN

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	N-OCTANE
Molecular weight formula_weight	114.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	DECYLAMINE-N,N-DIMETHYL-N-OXIDE
Molecular weight formula_weight	201.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 7 Entity 7 non-polymer

Description description	DODECANE
Molecular weight formula_weight	170.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	HEXANE
Molecular weight formula_weight	86.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 10 Entity 10 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	(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
Molecular weight formula_weight	457.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	(2S)-3-hydroxypropane-1,2-diyl didecanoate
Molecular weight formula_weight	400.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	DECANE
Molecular weight formula_weight	142.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 14 Entity 14 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 15 Entity 15 non-polymer

Description description	PENTADECANE
Molecular weight formula_weight	212.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 16 Entity 16 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 17 Entity 17 non-polymer

Description description	Octadecane
Molecular weight formula_weight	254.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 18 Entity 18 non-polymer

Description description	HEXADECANE
Molecular weight formula_weight	226.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 19 Entity 19 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 20 Entity 20 non-polymer

Description description	TETRADECANE
Molecular weight formula_weight	198.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 21 Entity 21 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 22 Entity 22 non-polymer

Description description	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
Molecular weight formula_weight	453.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 23 Entity 23 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 24 Entity 24 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1188

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6zo6B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

Domain ID domain_id	6zo6B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

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Unit-cell length a length_a	146.281 Å
Unit-cell length b length_b	161.008 Å
Unit-cell length c length_c	245.457 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	49.360 Å
R factor r_factor	0.2324
R_work r_work	0.2311
R_free r_free	0.2572

Minocycline binding to the deep binding pocket of AcrB-G619P

1. Protein Identity and Related Structures Protein Identity & Related Structures

Multidrug efflux pump subunit AcrB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6zo6__assembly_1__model_1

6zo6__assembly_1__model_1 | I(q)

6zo6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (24)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

Entity 15 Entity 15 non-polymer

Entity 16 Entity 16 non-polymer

Entity 17 Entity 17 non-polymer

Entity 18 Entity 18 non-polymer

Entity 19 Entity 19 non-polymer

Entity 20 Entity 20 non-polymer

Entity 21 Entity 21 non-polymer

Entity 22 Entity 22 non-polymer

Entity 23 Entity 23 non-polymer

Entity 24 Entity 24 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)