5DKV | pdb_00005dkv

Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET EFI-511225) bound with alpha-D-Tagatopyranose

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	d5dkva1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Allorhizobium ampelinum S4 ) [TaxId: 311402 ],	SCOPe (2.08)
A	d5dkva2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Allorhizobium ampelinum S4 ) [TaxId: 311402 ],	SCOPe (2.08)
B	d5dkvb_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Allorhizobium ampelinum S4 ) [TaxId: 311402 ],	SCOPe (2.08)
C	d5dkvc_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Allorhizobium ampelinum S4 ) [TaxId: 311402 ],	SCOPe (2.08)
D	d5dkvd_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Allorhizobium ampelinum S4 ) [TaxId: 311402 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type 1 solute binding protein-like	8071224	3000125	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 1 solute binding protein-like	8071224	3000125	SCOP2B (2022-06-29)
C	SCOP2 Family	L-arabinose binding protein-like	8071223	4000206	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Type 1 solute binding protein-like	8071224	3000125	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Type 1 solute binding protein-like	8071224	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)
A	Peripla_BP_4_C	e5dkvA1	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_4_N	e5dkvA2	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_N	ECOD (1.6)
B	Peripla_BP_4_C	e5dkvB1	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_4_N	e5dkvB2	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_N	ECOD (1.6)
C	Peripla_BP_4_C	e5dkvC1	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_4_N	e5dkvC2	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_N	ECOD (1.6)
D	Peripla_BP_4_C	e5dkvD1	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)
D	Peripla_BP_4_N	e5dkvD2	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_N	ECOD (1.6)

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	ABC transporter substrate binding protein (Ribose)	binding carbohydrate binding	-	cellular anatomical structure cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
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.