2RDD

X-ray crystal structure of AcrB in complex with a novel transmembrane helix.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB pore domain PN1, PN2, PC1 and PC2 subdomains	8042529	3000503	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB pore domain PN1, PN2, PC1 and PC2 subdomains	8042525	3000503	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB transmembrane domain	8042534	3000769	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB TolC docking domain (DN and DC subdomains)	8042533	3000526	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB pore domain PN1, PN2, PC1 and PC2 subdomains	8042525	3000503	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB transmembrane domain	8042534	3000769	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB transmembrane domain	8042535	3000769	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB pore domain PN1, PN2, PC1 and PC2 subdomains	8042528	3000503	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB transmembrane domain	8042535	3000769	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB TolC docking domain (DN and DC subdomains)	8042531	3000526	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Multidrug efflux transporter AcrB pore domain PN1, PN2, PC1 and PC2 subdomains	8042523	3000503	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ACR_tran_4th	e2rddA11	A: alpha bundles	X: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	H: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	T: Multidrug efflux transporter AcrB transmembrane domain	F: ACR_tran_4th	ECOD (1.6)
A	ACR_tran_1st	e2rddA12	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_1st	ECOD (1.6)
A	ACR_tran_5th	e2rddA13	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_5th	ECOD (1.6)
A	ACR_tran_3rd	e2rddA15	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_3rd	ECOD (1.6)
A	ACR_tran_6th	e2rddA14	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_6th	ECOD (1.6)
A	ACR_tran_2nd	e2rddA7	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB TolC docking domain	F: ACR_tran_2nd	ECOD (1.6)
A	ACR_tran_6th_1	e2rddA9	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB TolC docking domain	F: ACR_tran_6th_1	ECOD (1.6)
B	YajC	e2rddB1	A: extended segments	X: Preprotein translocase subunit YajC (From Topology)	H: Preprotein translocase subunit YajC (From Topology)	T: Preprotein translocase subunit YajC	F: YajC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1640.10	Mainly Alpha	Up-down Bundle	Multidrug efflux transporter AcrB transmembrane fold	Multidrug efflux transporter AcrB transmembrane domain	CATH (4.3.0)
A	3.30.70.1430	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Multidrug efflux transporter AcrB pore domain	CATH (4.3.0)
A	3.30.70.1320	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Multidrug efflux transporter AcrB pore domain like	CATH (4.3.0)
A	3.30.2090.10	Alpha Beta	2-Layer Sandwich	Multidrug efflux transporter AcrB TolC docking domain	DN and DC subdomains	CATH (4.3.0)
A	3.30.70.1440	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Multidrug efflux transporter AcrB pore domain	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A	ARO:3000216	acrB	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	CARD (3.3.0)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A	ARO:0010004	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic, cephalosporin, glycylcycline, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics	antibiotic efflux	CARD (3.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00873	AcrB/AcrD/AcrF family (ACR_tran)	AcrB/AcrD/AcrF family	-	Family
B	PF02699	Preprotein translocase subunit (YajC)	Preprotein translocase subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Acriflavine resistance protein B	alkane transmembrane transporter activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity organic hydroxy compound transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity organic acid transmembrane transporter activity organic anion transmembrane transporter activity bile acid transmembrane transporter activity efflux transmembrane transporter activity xenobiotic transmembrane transporter activity identical protein binding alkane transmembrane transporter activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity organic hydroxy compound transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity organic acid transmembrane transporter activity organic anion transmembrane transporter activity bile acid transmembrane transporter activity efflux transmembrane transporter activity xenobiotic transmembrane transporter activity identical protein binding protein binding binding enterobactin transmembrane transporter activity siderophore-iron transmembrane transporter activity	response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process organic anion transport response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process organic anion transport carboxylic acid transport lipid localization lipid transport organic acid transport monocarboxylic acid transport fatty acid transport macromolecule localization alkane transport response to antibiotic bile acid and bile salt transport organic hydroxy compound transport siderophore transport iron ion transport metal ion transport enterobactin transport transition metal ion transport monoatomic ion transport monoatomic cation transport iron coordination entity transport	cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery plasma membrane cell surface periplasmic side of plasma membrane external side of plasma membrane side of membrane
B	UPF0092 membrane protein yajC	-	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process membrane organization establishment of protein localization to membrane localization within membrane protein localization to membrane cellular component organization protein insertion into membrane from inner side cellular component organization or biogenesis protein insertion into membrane	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027463	Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains	Homologous Superfamily
A	IPR001036	Acriflavin resistance protein	Family
A	IPR004764	Multidrug resistance protein MdtF-like	Family
B	IPR003849	Preprotein translocase YajC	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	Resistance-nodulation-cell division	Hydrophobe/amphiphile efflux-1 family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Multi-Drug Efflux Transporters	AcrB bacterial multi-drug efflux transporter with YajC subunit

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.