1URP | pdb_00001urp

D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1urpd_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	D-ribose-binding protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1urpc_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	D-ribose-binding protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1urpb_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	D-ribose-binding protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d1urpa_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	D-ribose-binding protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Type 1 solute binding protein-like	8033251	3000125	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 1 solute binding protein-like	8033251	3000125	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 1 solute binding protein-like	8033251	3000125	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type 1 solute binding protein-like	8033251	3000125	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	Peripla_BP_1_1st	e1urpD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st	ECOD (1.6)
D	Peripla_BP_4_C	e1urpD3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_C	ECOD (1.6)
C	Peripla_BP_1_1st	e1urpC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st	ECOD (1.6)
C	Peripla_BP_4_C	e1urpC3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_C	ECOD (1.6)
B	Peripla_BP_1_1st	e1urpB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st	ECOD (1.6)
B	Peripla_BP_4_C	e1urpB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_C	ECOD (1.6)
A	Peripla_BP_1_1st	e1urpA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st	ECOD (1.6)
A	Peripla_BP_4_C	e1urpA3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13407	Periplasmic binding protein domain (Peripla_BP_4)	Periplasmic binding protein domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-RIBOSE-BINDING PROTEIN	binding monosaccharide binding carbohydrate binding small molecule binding	transmembrane transport localization pentose transmembrane transport transport D-ribose transmembrane transport carbohydrate transport cellular process monosaccharide transmembrane transport carbohydrate transmembrane transport establishment of localization positive chemotaxis chemotaxis response to stimulus taxis transmembrane transport localization pentose transmembrane transport transport D-ribose transmembrane transport carbohydrate transport cellular process monosaccharide transmembrane transport carbohydrate transmembrane transport establishment of localization positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing 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 outer membrane-bounded periplasmic space cell envelope ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing 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 outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR025997	Periplasmic binding protein	Domain
A, B, C, D	IPR028082	Periplasmic binding protein-like I	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.