1VR5 | pdb_00001vr5

Crystal structure of Oligopeptide ABC transporter, periplasmic oligopeptide-binding (TM1223) from THERMOTOGA MARITIMA at 1.73 A resolution

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)
A	d1vr5a1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Oligo-peptide binding protein (OPPA)	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d1vr5a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vr5b2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Oligo-peptide binding protein (OPPA)	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vr5b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	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	8020313	4000229	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type 2 solute binding protein-like	8032693	3000083	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8032693	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		e1vr5A3	A: all-alpha NTP pyrophosphatases	X: all-alpha NTP pyrophosphatases	H: MazG-related	T: MazG	F:	ECOD (20:10:01)
B		e1vr5B1	A: HTH	X: HTH	H: winged helix domain	T: Rv3651-like_N	F:	ECOD (20:10:01)
B		e1vr5B2	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: DctP	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 (4.3.0)
A	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
A	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
B	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00496	Bacterial extracellular solute-binding proteins, family 5 Middle (SBP_bac_5)	Bacterial extracellular solute-binding proteins, family 5 Middle	The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein	peptide transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	peptide 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 periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000914	Solute-binding protein family 5 domain	Domain
A, B	IPR039424	Solute-binding protein family 5	Family
A, B	IPR030678	Peptide/nickel binding protein, MppA-type	Family

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.