7NDF | pdb_00007ndf

Crystal structure of nanobody Nb_MsbA#1 in complex with the nucleotide binding domain of MsbA

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth D]	V-set_1	e7ndfD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
A [auth C]	V-set_1	e7ndfC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
D [auth B]	ABC_tran_1	e7ndfB1	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 [auth A]	ABC_tran_1	e7ndfA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	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 [auth C], B [auth D]	Nb_MsbA 1	-	-	-
C [auth A], D [auth B]	Lipid A ABC transporter ATP-binding protein/permease MsbA	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 lipid transporter activity lipid transmembrane transporter activity ATPase-coupled lipid transmembrane transporter activity lipid binding 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 ATPase-coupled intramembrane lipid transporter activity intramembrane lipid transporter activity lipopolysaccharide floppase activity floppase activity identical protein binding protein binding	localization transport macromolecule localization lipid localization lipid transport establishment of localization lipopolysaccharide transport carbohydrate derivative transport membrane organization biological regulation lipid translocation regulation of membrane lipid distribution cellular component organization cellular process localization transport macromolecule localization lipid localization lipid transport establishment of localization lipopolysaccharide transport carbohydrate derivative transport membrane organization biological regulation lipid translocation regulation of membrane lipid distribution cellular component organization cellular process cellular component organization or biogenesis regulation of biological quality transmembrane transport	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex MsbA transporter complex

InterPro: Protein Family Classification InterPro Database Homepage

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

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.