5NIL | pdb_00005nil

Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	GBAA_5634-like	8106452	3002779	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	GBAA_5634-like	8106452	3002779	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	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)
D	HlyD_D23_C	e5nilD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
D	8a0102	e5nilD3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: 8a0102	ECOD (1.6)
D	HlyD_2nd	e5nilD4	A: alpha bundles	X: helical hairpin of HlyD-like secretion proteins (From Topology)	H: helical hairpin of HlyD-like secretion proteins (From Topology)	T: helical hairpin of HlyD-like secretion proteins	F: HlyD_2nd	ECOD (1.6)
D	Biotin_lipoyl_1	e5nilD2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_1	ECOD (1.6)
E	HlyD_D23_C	e5nilE3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
E	8a0102	e5nilE4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: 8a0102	ECOD (1.6)
E	HlyD_2nd	e5nilE2	A: alpha bundles	X: helical hairpin of HlyD-like secretion proteins (From Topology)	H: helical hairpin of HlyD-like secretion proteins (From Topology)	T: helical hairpin of HlyD-like secretion proteins	F: HlyD_2nd	ECOD (1.6)
E	Biotin_lipoyl_1	e5nilE1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_1	ECOD (1.6)
F	HlyD_D23_C	e5nilF4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
F	8a0102	e5nilF3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: 8a0102	ECOD (1.6)
F	HlyD_2nd	e5nilF1	A: alpha bundles	X: helical hairpin of HlyD-like secretion proteins (From Topology)	H: helical hairpin of HlyD-like secretion proteins (From Topology)	T: helical hairpin of HlyD-like secretion proteins	F: HlyD_2nd	ECOD (1.6)
F	Biotin_lipoyl_1	e5nilF2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_1	ECOD (1.6)
G	HlyD_D23_C	e5nilG2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
G	8a0102	e5nilG4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: 8a0102	ECOD (1.6)
G	HlyD_2nd	e5nilG1	A: alpha bundles	X: helical hairpin of HlyD-like secretion proteins (From Topology)	H: helical hairpin of HlyD-like secretion proteins (From Topology)	T: helical hairpin of HlyD-like secretion proteins	F: HlyD_2nd	ECOD (1.6)
G	Biotin_lipoyl_1	e5nilG3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_1	ECOD (1.6)
H	HlyD_D23_C	e5nilH4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
H	8a0102	e5nilH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: 8a0102	ECOD (1.6)
H	HlyD_2nd	e5nilH2	A: alpha bundles	X: helical hairpin of HlyD-like secretion proteins (From Topology)	H: helical hairpin of HlyD-like secretion proteins (From Topology)	T: helical hairpin of HlyD-like secretion proteins	F: HlyD_2nd	ECOD (1.6)
H	Biotin_lipoyl_1	e5nilH3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_1	ECOD (1.6)
I	HlyD_D23_C	e5nilI3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
I	8a0102	e5nilI2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: 8a0102	ECOD (1.6)
I	HlyD_2nd	e5nilI4	A: alpha bundles	X: helical hairpin of HlyD-like secretion proteins (From Topology)	H: helical hairpin of HlyD-like secretion proteins (From Topology)	T: helical hairpin of HlyD-like secretion proteins	F: HlyD_2nd	ECOD (1.6)
I	Biotin_lipoyl_1	e5nilI1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_1	ECOD (1.6)
A	OEP	e5nilA1	A: a+b duplicates or obligate multimers	X: Outer membrane efflux proteins (OEP) (From Topology)	H: Outer membrane efflux proteins (OEP) (From Topology)	T: Outer membrane efflux proteins (OEP)	F: OEP	ECOD (1.6)
B	OEP	e5nilB1	A: a+b duplicates or obligate multimers	X: Outer membrane efflux proteins (OEP) (From Topology)	H: Outer membrane efflux proteins (OEP) (From Topology)	T: Outer membrane efflux proteins (OEP)	F: OEP	ECOD (1.6)
C	OEP	e5nilC1	A: a+b duplicates or obligate multimers	X: Outer membrane efflux proteins (OEP) (From Topology)	H: Outer membrane efflux proteins (OEP) (From Topology)	T: Outer membrane efflux proteins (OEP)	F: OEP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
J, K	PF12704	MacB-like periplasmic core domain (MacB_PCD)	MacB-like periplasmic core domain	This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein [1]. Some structural similarity was found to the periplasmic domain of the AcrB multidrug eff ...	This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein [1]. Some structural similarity was found to the periplasmic domain of the AcrB multidrug efflux transporter.	Domain
J, K	PF02687	FtsX-like permease C-terminal (FtsX)	FtsX-like permease C-terminal	This entry represents the C-terminal helices found in members of the ABC type 3 transporter family of permeases, including Cell division protein FtsX from Gram-negative and Gram-positive bacteria [1], Permease protein MacB [2], Lipoprotein-releasing ...	This entry represents the C-terminal helices found in members of the ABC type 3 transporter family of permeases, including Cell division protein FtsX from Gram-negative and Gram-positive bacteria [1], Permease protein MacB [2], Lipoprotein-releasing system transmembrane protein LolC (Swiss:P57382) which has been shown to transport lipids targeted to the outer membrane across the inner membrane [3]. This region contains three transmembrane helices.	Domain
J, K	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain
A, B, C	PF02321	Outer membrane efflux protein (OEP)	Outer membrane efflux protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J, K	Macrolide export ATP-binding/permease protein MacB	xenobiotic transmembrane transporter activity ABC-type transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type xenobiotic transporter activity transporter activity transmembrane transporter activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding xenobiotic transmembrane transporter activity ABC-type transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type xenobiotic transporter activity transporter activity transmembrane transporter activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity polymyxin transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity amide transmembrane transporter activity	response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport amide transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport amide transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane detoxification export from cell export across plasma membrane response to toxic substance transmembrane transport cellular process	cellular anatomical structure membrane cell periphery plasma membrane protein-containing complex transmembrane transporter complex MacAB-TolC complex membrane protein complex macrolide transmembrane transporter complex transporter complex
D, E, F, G, H D, E, F, G, H, I	Macrolide export protein MacA	polymyxin transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity amide transmembrane transporter activity transporter activity transmembrane transporter activity efflux transmembrane transporter activity identical protein binding protein binding binding	response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport amide transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport amide transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane detoxification export from cell export across plasma membrane response to toxic substance transmembrane transport cellular process	cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery plasma membrane MacAB-TolC complex macrolide transmembrane transporter complex extrinsic component of membrane
A, B, C	Outer membrane protein TolC	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity monoatomic ion channel activity monoatomic ion transmembrane transporter activity efflux transmembrane transporter activity wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity monoatomic ion channel activity monoatomic ion transmembrane transporter activity efflux transmembrane transporter activity identical protein binding protein binding binding enterobactin transmembrane transporter activity siderophore-iron transmembrane transporter activity iron chelate 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 response to antibiotic 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 response to antibiotic monoatomic ion transmembrane transport monoatomic ion transport organic anion transport carboxylic acid transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport organic acid transport monocarboxylic acid transport macromolecule localization siderophore transport iron ion transport metal ion transport enterobactin transport transition metal ion transport monoatomic cation transport iron coordination entity transport xenobiotic export from cell xenobiotic detoxification by transmembrane export across the plasma membrane export from cell export across plasma membrane	cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane MacAB-TolC complex cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane MacAB-TolC complex macrolide transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope periplasmic space cell outer membrane external encapsulating structure outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J, K	IPR050250	Macrolide Exporter MacB	Family
J, K	IPR017871	ABC transporter-like, conserved site	Conserved Site
J, K	IPR017911	MacB-like, ATP-binding domain	Domain
J, K	IPR003838	ABC3 transporter permease, C-terminal	Domain
J, K	IPR003439	ABC transporter-like, ATP-binding domain	Domain
J, K	IPR003593	AAA+ ATPase domain	Domain
J, K	IPR025857	MacB-like periplasmic core domain	Domain
J, K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D, E, F, G, H D, E, F, G, H, I	IPR030190	Macrolide export protein MacA, alpha-hairpin domain superfamily	Homologous Superfamily
D, E, F, G, H D, E, F, G, H, I	IPR006143	RND efflux pump, membrane fusion protein	Family
D, E, F, G, H D, E, F, G, H, I	IPR032317	CusB_D23	Unknown
A, B, C	IPR010130	Type I secretion outer membrane protein, TolC	Family
A, B, C	IPR051906	Outer membrane protein TolC-like	Family
A, B, C	IPR003423	Outer membrane efflux protein	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	ATP Binding Cassette (ABC) Transporters	MacAB-TolC tripartite multidrug efflux pump, MacA-TolC section