4YMT | pdb_00004ymt

Crystal structure of an amino acid ABC transporter complex with arginines

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth A]	d4ymta_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)
A [auth J]	d4ymtj_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth B]	e4ymtB1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: FlaF_Ig-like	F:	ECOD (20:10:01)
C	e4ymtC1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: FlaF_Ig-like	F:	ECOD (20:10:01)
B [auth A]	e4ymtA1	A: Bromodomain-like	X: HTH	H: Three-helical HTH	T: LAGLIDADG_1	F:	ECOD (20:10:01)
A [auth J]	e4ymtJ1	A: Bromodomain-like	X: HTH	H: Three-helical HTH	T: LAGLIDADG_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	1.10.3720.10	Mainly Alpha	Orthogonal Bundle	MetI-like fold	MetI-like	CATH (4.3.0)
C	1.10.3720.10	Mainly Alpha	Orthogonal Bundle	MetI-like fold	MetI-like	CATH (4.3.0)
B [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth J]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D [auth B]	PF00528	Binding-protein-dependent transport system inner membrane component (BPD_transp_1)	Binding-protein-dependent transport system inner membrane component	-	Family
A [auth J], B [auth A]	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
C, D [auth B]	ABC-type amino acid transport system, permease component	transporter activity transmembrane transporter activity	amino acid transport localization transport establishment of localization	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
A [auth J], B [auth A]	ABC-type polar amino acid transport system, ATPase component	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 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 ATP-dependent activity amino acid transmembrane transporter activity ABC-type amino acid transporter activity ABC-type transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity transporter activity transmembrane transporter activity cation binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D [auth B]	IPR000515	ABC transporter type 1, transmembrane domain MetI-like	Domain
C, D [auth B]	IPR035906	MetI-like superfamily	Homologous Superfamily
C, D [auth B]	IPR043429	ABC transporter membrane protein permease protein ArtM/GltK/GlnP/TcyL/YhdX-like	Family
C, D [auth B]	IPR010065	Amino acid ABC transporter, permease protein, 3-TM domain	Domain
A [auth J], B [auth A]	IPR003593	AAA+ ATPase domain	Domain
A [auth J], B [auth A]	IPR017871	ABC transporter-like, conserved site	Conserved Site
A [auth J], B [auth A]	IPR030679	ABC-type amino acid transport system, ATPase component, HisP-type	Family
A [auth J], B [auth A]	IPR003439	ABC transporter-like, ATP-binding domain	Domain
A [auth J], B [auth A]	IPR050086	Methionine import ATP-binding protein MetN-like	Family
A [auth J], B [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C, D [auth B]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
C, D [auth B]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C, D [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	ATP Binding Cassette (ABC) Transporters	Art(QN)₂ amino acid importer

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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