4YMX | pdb_00004ymx

Crystal structure of the substrate binding protein of an amino acid ABC transporter

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
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)
A	d4ymxa_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)
B	d4ymxb_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Phosphate binding protein-like	8071149	4000229	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type 2 solute binding protein-like	8071150	3000083	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8071150	3000083	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		e4ymxA1	A: Bromodomain-like	X: HTH	H: Three-helical HTH	T: LAGLIDADG_1	F:	ECOD (20:10:01)
B		e4ymxB1	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)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00497	Bacterial extracellular solute-binding proteins, family 3 (SBP_bac_3)	Bacterial extracellular solute-binding proteins, family 3	This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. Thi ...	This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognises Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ABC-type amino acid transport system, periplasmic component	ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	-	cellular anatomical structure membrane cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018313	Solute-binding protein family 3, conserved site	Conserved Site
A, B	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, 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.