4dx5

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

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 heterocomplex	Heteromer	Protein 5	DARPIN × 2 GLYCEROL × 15 DODECYL-BETA-D-MALTOSIDE × 8 N-OCTANE × 7 DECANE × 6 HEXANE × 5 DODECANE × 4 (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 TETRADECANE × 1 DODECYL-ALPHA-D-MALTOSIDE × 1 nonane × 1 SULFATE ION × 1 UNDECANE × 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	4dx5
Deposition date deposition_date	2012-02-27
Structure title title	Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop
Keywords keywords	DARPin, multidrug efflux protein, MEMBRANE PROTEIN, TRANSPORT PROTEIN; MEMBRANE 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.

4dx5__assembly_1__model_1

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

Download this curve (.dat)

4dx5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dx5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.70 Å
Rg (electron density)	47.11 Å
Total Rg	47.33 Å
Atom count	27227
Residues	3418
Excluded volume	483470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dx5__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 (15)

Entity 1 Entity 1 polymer

Description description	Acriflavine resistance protein B
Molecular weight formula_weight	114736.3 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	29010

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHHLEHHHHHH

Source Source

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

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
Common name common_name	ARTIFICIAL GENE
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 4 Entity 4 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	N-OCTANE
Molecular weight formula_weight	114.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	DECANE
Molecular weight formula_weight	142.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	HEXANE
Molecular weight formula_weight	86.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 non-polymer

Description description	DODECANE
Molecular weight formula_weight	170.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 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 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	DODECYL-ALPHA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	nonane
Molecular weight formula_weight	128.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

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

Entity 14 Entity 14 non-polymer

Description description	UNDECANE
Molecular weight formula_weight	156.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1783

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6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

Domain ID domain_id	4dx5A01
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	4dx5A02
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	4dx5A03
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	4dx5A04
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	4dx5A05
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	4dx5A06
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	4dx5A07
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	4dx5A08
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	4dx5B01
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	4dx5B02
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	4dx5B03
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	4dx5B04
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	4dx5B05
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	4dx5B06
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	4dx5B07
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	4dx5B08
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	4dx5C01
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	4dx5C02
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	4dx5C03
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	4dx5C04
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	4dx5C05
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	4dx5C06
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	4dx5C07
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	4dx5C08
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	4dx5D00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	4dx5E00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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Unit-cell length a length_a	145.990 Å
Unit-cell length b length_b	161.720 Å
Unit-cell length c length_c	245.970 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	1.900 Å
Low-resolution limit resolution_low	39.468 Å
R factor r_factor	0.2018
R_work r_work	0.2002
R_free r_free	0.2312

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

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

4dx5__assembly_1__model_1

4dx5__assembly_1__model_1 | I(q)

4dx5__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 (15)

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 water

6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

7. Citations (1)

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

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

4dx5__assembly_1__model_1

4dx5__assembly_1__model_1 | I(q)

4dx5__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 (15)

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 water

6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

7. Citations (1)