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)
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)
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)
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)
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)

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	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)
B	SCOP2B Superfamily	Type 1 solute binding protein-like	8071224	3000125	SCOP2B (2022-06-29)
A	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)
D	EF-hand_1, EF-hand_5, EF-hand_7	e5dkvD1	A: a/b three-layered sandwiches	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.1)
C	EF-hand_1, EF-hand_5, EF-hand_7	e5dkvC1	A: a/b three-layered sandwiches	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.1)
B	EF-hand_1, EF-hand_5, EF-hand_7	e5dkvB1	A: a/b three-layered sandwiches	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.1)
A	EF-hand_1, EF-hand_5, EF-hand_7	e5dkvA1	A: a/b three-layered sandwiches	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.1)

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