4zjo

Crystal structure of AcrB triple mutant in complex with antibiotic in P21 space group

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 str. K-12 substr. MG1655

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ERYTHROMYCIN A × 1 DODECYL-BETA-D-MALTOSIDE × 4 NICKEL (II) ION × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	ERYTHROMYCIN A × 1 DODECYL-BETA-D-MALTOSIDE × 4 NICKEL (II) ION × 1	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 Author chain D； PDBConstruct 1–1049； UniProt 1–1049 Author chain E； PDBConstruct 1–1049； UniProt 1–1049 Author chain F； 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	4zjo
Deposition date deposition_date	2015-04-29
Structure title title	Crystal structure of AcrB triple mutant in complex with antibiotic in P21 space group
Keywords keywords	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.

4zjo__assembly_1__model_1

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

Download this curve (.dat)

4zjo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zjo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.43 Å
Rg (electron density)	45.71 Å
Total Rg	46.02 Å
Atom count	23931
Residues	3128
Excluded volume	432480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zjo__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4zjo__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Multidrug efflux pump subunit AcrB
Molecular weight formula_weight	113426.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	47876

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGAGAAGAGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH

Source Source

Source organism organism	Escherichia coli str. K-12 substr. MG1655
NCBI taxonomy ID ncbi_taxonomy_id	511145
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ERYTHROMYCIN A
Molecular weight formula_weight	733.9 kDa
Source method src_method	syn
Copy count entity_count	2

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	8

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

Domain ID domain_id	4zjoA01
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	4zjoA02
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	4zjoA03
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	4zjoA04
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	4zjoA05
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	4zjoA06
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	4zjoA07
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	4zjoA08
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	4zjoB01
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	4zjoB02
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	4zjoB03
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	4zjoB04
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	4zjoB05
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	4zjoB06
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	4zjoB07
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	4zjoB08
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	4zjoC01
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	4zjoC02
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	4zjoC03
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	4zjoC04
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	4zjoC05
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	4zjoC06
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	4zjoC07
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	4zjoC08
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	4zjoD01
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	4zjoD02
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	4zjoD03
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	4zjoD04
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	4zjoD05
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	4zjoD06
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	4zjoD07
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	4zjoD08
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	4zjoE01
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	4zjoE02
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	4zjoE03
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	4zjoE04
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	4zjoE05
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	4zjoE06
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	4zjoE07
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	4zjoE08
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	4zjoF01
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	4zjoF02
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	4zjoF03
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	4zjoF04
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	4zjoF05
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	4zjoF06
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	4zjoF07
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	4zjoF08
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	151.184 Å
Unit-cell length b length_b	156.769 Å
Unit-cell length c length_c	218.168 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	19.957 Å
R factor r_factor	0.2414
R_work r_work	0.2378
R_free r_free	0.3067

Crystal structure of AcrB triple mutant in complex with antibiotic in P21 space group

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4zjo__assembly_1__model_1

4zjo__assembly_1__model_1 | I(q)

4zjo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

7. Citations (1)

Crystal structure of AcrB triple mutant in complex with antibiotic in P21 space group

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

4zjo__assembly_1__model_1

4zjo__assembly_1__model_1 | I(q)

4zjo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

7. Citations (1)