3B5Y

Crystal Structure of MsbA from Salmonella typhimurium with AMPPNP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3b5yd1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	ABC transporter ATPase domain-like	Multidrug resistance ABC transporter MsbA, C-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
D	d3b5yd2	Membrane and cell surface proteins and peptides	ABC transporter transmembrane region	ABC transporter transmembrane region	ABC transporter transmembrane region	Multidrug resistance ABC transporter MsbA, N-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
A	d3b5ya1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	ABC transporter ATPase domain-like	Multidrug resistance ABC transporter MsbA, C-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
A	d3b5ya2	Membrane and cell surface proteins and peptides	ABC transporter transmembrane region	ABC transporter transmembrane region	ABC transporter transmembrane region	Multidrug resistance ABC transporter MsbA, N-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d3b5yb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	ABC transporter ATPase domain-like	Multidrug resistance ABC transporter MsbA, C-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d3b5yb2	Membrane and cell surface proteins and peptides	ABC transporter transmembrane region	ABC transporter transmembrane region	ABC transporter transmembrane region	Multidrug resistance ABC transporter MsbA, N-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
C	d3b5yc1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	ABC transporter ATPase domain-like	Multidrug resistance ABC transporter MsbA, C-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
C	d3b5yc2	Membrane and cell surface proteins and peptides	ABC transporter transmembrane region	ABC transporter transmembrane region	ABC transporter transmembrane region	Multidrug resistance ABC transporter MsbA, N-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	ABC transporter transmembrane region-like	8057793	3001546	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8057798	3002020	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8057798	3002020	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ABC transporter transmembrane region-like	8057793	3001546	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8057798	3002020	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ABC transporter transmembrane region-like	8057793	3001546	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8057798	3002020	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ABC transporter transmembrane region-like	8057793	3001546	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	ABC_membrane	e3b5yD2	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type I ABC exporter transmembrane domain fold (From Topology)	T: Type I ABC exporter transmembrane domain fold	F: ABC_membrane	ECOD (1.6)
D	ABC_tran_1	e3b5yD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran_1	ECOD (1.6)
A	ABC_membrane	e3b5yA2	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type I ABC exporter transmembrane domain fold (From Topology)	T: Type I ABC exporter transmembrane domain fold	F: ABC_membrane	ECOD (1.6)
A	ABC_tran_1	e3b5yA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran_1	ECOD (1.6)
B	ABC_membrane	e3b5yB2	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type I ABC exporter transmembrane domain fold (From Topology)	T: Type I ABC exporter transmembrane domain fold	F: ABC_membrane	ECOD (1.6)
B	ABC_tran_1	e3b5yB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran_1	ECOD (1.6)
C	ABC_membrane	e3b5yC2	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type I ABC exporter transmembrane domain fold (From Topology)	T: Type I ABC exporter transmembrane domain fold	F: ABC_membrane	ECOD (1.6)
C	ABC_tran_1	e3b5yC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran_1	ECOD (1.6)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B, C, D	ARO:3003950	msbA	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A, a major component of the bacterial outer cell membrane, and is the only bacterial ABC transporter that is essential for cell viability.	CARD (4.0.0)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B, C, D	ARO:0010001	ATP-binding cassette (ABC) antibiotic efflux pump	nitroimidazole antibiotic	antibiotic efflux	CARD (4.0.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00664	ABC transporter transmembrane region (ABC_membrane)	ABC transporter transmembrane region	-	Family
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lipid A export ATP-binding/permease protein msbA	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 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 lipid transporter activity active transmembrane transporter activity lipid transmembrane transporter activity ATPase-coupled lipid transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity transporter activity transmembrane transporter activity ATP-dependent activity ABC-type transporter 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 identical protein binding protein binding	transmembrane transport localization transport cellular process establishment of localization	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017871	ABC transporter-like, conserved site	Conserved Site
A, B, C, D	IPR003439	ABC transporter-like, ATP-binding domain	Domain
A, B, C, D	IPR036640	ABC transporter type 1, transmembrane domain superfamily	Homologous Superfamily
A, B, C, D	IPR011917	ABC transporter, lipid A-core flippase, MsbA	Family
A, B, C, D	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D	IPR011527	ABC transporter type 1, transmembrane domain	Domain
A, B, C, D	IPR039421	Type 1 protein exporter	Family
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	ATP Binding Cassette (ABC) Transporters	MsbA Lipid "flippase" with bound AMPPNP

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.