3aob

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

Method: X-RAY DIFFRACTION

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

Acriflavine resistance protein B

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	RIFAMPICIN × 1 water × 3	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	3aob
Deposition date deposition_date	2010-09-23
Structure title title	Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket
Keywords keywords	Membrane Protein, Inner Membrane, MEMBRANE PROTEIN-ANTIBIOTIC complex; MEMBRANE PROTEIN/ANTIBIOTIC
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.

3aob__assembly_1__model_1

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

Download this curve (.dat)

3aob__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3aob__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.45 Å
Rg (electron density)	44.87 Å
Total Rg	45.20 Å
Atom count	23381
Residues	3066
Excluded volume	422620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3aob__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Acriflavine resistance protein B
Molecular weight formula_weight	114217.7 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	23385

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	RIFAMPICIN
Molecular weight formula_weight	822.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	3aobA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	3aobA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1320 — Multidrug efflux transporter AcrB pore domain like

Domain ID domain_id	3aobA04
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	3aobA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	3aobA06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobA07
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1440 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobA08
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	3aobB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	3aobB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1320 — Multidrug efflux transporter AcrB pore domain like

Domain ID domain_id	3aobB04
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	3aobB05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	3aobB06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobB07
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1440 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobB08
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	3aobC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	3aobC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1320 — Multidrug efflux transporter AcrB pore domain like

Domain ID domain_id	3aobC04
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	3aobC05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	3aobC06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobC07
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1440 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	3aobC08
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	223.897 Å
Unit-cell length b length_b	134.314 Å
Unit-cell length c length_c	161.766 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.350 Å
Low-resolution limit resolution_low	48.910 Å
R factor r_factor	0.2642
R_work r_work	0.2608
R_free r_free	0.3256

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

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

Acriflavine resistance protein B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3aob__assembly_1__model_1

3aob__assembly_1__model_1 | I(q)

3aob__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

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

Acriflavine resistance protein B

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

3aob__assembly_1__model_1

3aob__assembly_1__model_1 | I(q)

3aob__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)