2BSD | pdb_00002bsd

Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein

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	d2bsda1	All beta proteins	Virus attachment protein globular domain	Virus attachment protein globular domain	Lactophage receptor-binding protein head domain	receptor binding protein, rbp, C-terminal domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
A	d2bsda2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	Lactophage receptor-binding protein domain	Receptor binding protein, rbp, middle domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
A	d2bsda3	All beta proteins	Pseudo beta-prism I	Bacteriophage trimeric proteins domain	Lactophage receptor-binding protein N-terminal domain	Receptor binding protein, rbp, N-terminal domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
B	d2bsdb1	All beta proteins	Virus attachment protein globular domain	Virus attachment protein globular domain	Lactophage receptor-binding protein head domain	receptor binding protein, rbp, C-terminal domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
B	d2bsdb2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	Lactophage receptor-binding protein domain	Receptor binding protein, rbp, middle domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
B	d2bsdb3	All beta proteins	Pseudo beta-prism I	Bacteriophage trimeric proteins domain	Lactophage receptor-binding protein N-terminal domain	Receptor binding protein, rbp, N-terminal domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
C	d2bsdc1	All beta proteins	Virus attachment protein globular domain	Virus attachment protein globular domain	Lactophage receptor-binding protein head domain	receptor binding protein, rbp, C-terminal domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
C	d2bsdc2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	Lactophage receptor-binding protein domain	Receptor binding protein, rbp, middle domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)
C	d2bsdc3	All beta proteins	Pseudo beta-prism I	Bacteriophage trimeric proteins domain	Lactophage receptor-binding protein N-terminal domain	Receptor binding protein, rbp, N-terminal domain	(Peduovirus P2 ) [TaxId: 10679 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phage fibre proteins	8036192	3000351	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Virus attachment protein globular domain	8036189	3001376	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacteriophage trimeric proteins domain	8036194	3000915	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phage fibre proteins	8036192	3000351	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Virus attachment protein globular domain	8036189	3001376	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacteriophage trimeric proteins domain	8036194	3000915	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Virus attachment protein globular domain	8036189	3001376	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacteriophage trimeric proteins domain	8036194	3000915	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phage fibre proteins	8036192	3000351	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	Caudo_bapla_RBP_1st_1,Caudo_bapla_RBP_1st	e2bsdA2	A: beta sandwiches	X: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	H: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	T: Lactophage receptor-binding protein N-terminal domain-like	F: Caudo_bapla_RBP_1st_1,Caudo_bapla_RBP_1st	ECOD (1.6)
A	Caudo_bapla_RBP_3rd	e2bsdA1	A: beta sandwiches	X: Domain in virus attachment proteins (From Topology)	H: Domain in virus attachment proteins (From Topology)	T: Domain in virus attachment proteins	F: Caudo_bapla_RBP_3rd	ECOD (1.6)
A	Caudo_bapla_RBP_1st_1	e2bsdA4	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: Caudo_bapla_RBP_1st_1	ECOD (1.6)
A	Caudo_bapla_RBP_like	e2bsdA3	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: Caudo_bapla_RBP_like	ECOD (1.6)
B	Caudo_bapla_RBP_1st_1,Caudo_bapla_RBP_1st	e2bsdB2	A: beta sandwiches	X: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	H: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	T: Lactophage receptor-binding protein N-terminal domain-like	F: Caudo_bapla_RBP_1st_1,Caudo_bapla_RBP_1st	ECOD (1.6)
B	Caudo_bapla_RBP_3rd	e2bsdB1	A: beta sandwiches	X: Domain in virus attachment proteins (From Topology)	H: Domain in virus attachment proteins (From Topology)	T: Domain in virus attachment proteins	F: Caudo_bapla_RBP_3rd	ECOD (1.6)
B	Caudo_bapla_RBP_1st_1	e2bsdB4	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: Caudo_bapla_RBP_1st_1	ECOD (1.6)
B	Caudo_bapla_RBP_like	e2bsdB3	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: Caudo_bapla_RBP_like	ECOD (1.6)
C	Caudo_bapla_RBP_1st_1,Caudo_bapla_RBP_1st	e2bsdC2	A: beta sandwiches	X: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	H: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	T: Lactophage receptor-binding protein N-terminal domain-like	F: Caudo_bapla_RBP_1st_1,Caudo_bapla_RBP_1st	ECOD (1.6)
C	Caudo_bapla_RBP_3rd	e2bsdC1	A: beta sandwiches	X: Domain in virus attachment proteins (From Topology)	H: Domain in virus attachment proteins (From Topology)	T: Domain in virus attachment proteins	F: Caudo_bapla_RBP_3rd	ECOD (1.6)
C	Caudo_bapla_RBP_1st_1	e2bsdC4	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: Caudo_bapla_RBP_1st_1	ECOD (1.6)
C	Caudo_bapla_RBP_like	e2bsdC3	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: Caudo_bapla_RBP_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.520.10	Mainly Beta	Sandwich	Triple-stranded beta-helix	Phage fibre proteins	CATH (4.3.0)
A	2.60.40.1830	Mainly Beta	Sandwich	Immunoglobulin-like	Phage tail base-plate Siphoviridae RBP, head domain	CATH (4.3.0)
B	2.60.520.10	Mainly Beta	Sandwich	Triple-stranded beta-helix	Phage fibre proteins	CATH (4.3.0)
B	2.60.40.1830	Mainly Beta	Sandwich	Immunoglobulin-like	Phage tail base-plate Siphoviridae RBP, head domain	CATH (4.3.0)
C	2.60.520.10	Mainly Beta	Sandwich	Triple-stranded beta-helix	Phage fibre proteins	CATH (4.3.0)
C	2.60.40.1830	Mainly Beta	Sandwich	Immunoglobulin-like	Phage tail base-plate Siphoviridae RBP, head domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF21564	Lactococcus phage p2, Receptor binding protein, neck domain (Caudo_bapla_RBP_neck)	Lactococcus phage p2, Receptor binding protein, neck domain	This domain is found centrally located in Receptor binding protein from Lactococcus phage p2 (RBP, also known as Gp18) and similar proteins from closely related lactococcal phages. RBP shows three domains: the N-terminal shoulder domain (Pfam:PF20747 ...	This domain is found centrally located in Receptor binding protein from Lactococcus phage p2 (RBP, also known as Gp18) and similar proteins from closely related lactococcal phages. RBP shows three domains: the N-terminal shoulder domain (Pfam:PF20747), which is attached to the phage, the neck domain (this entry) and the C -terminal receptor-recognition head domain (Pfam:PF08931). The central domain folds into four beta-strands, which interlace with the beta-strands of two other subunits to form an equilateral triangular prism around the three-fold axis of a triple-stranded beta-helix [1,2].	Domain
A, B, C	PF20747	Lactophage receptor-binding protein N-terminal shoulder domain (Caudo_bapla_N)	Lactophage receptor-binding protein N-terminal shoulder domain	Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein domain, shoulder, neck, and head, that form the phage tail base-plate. This entry represents the shoulder domain. This domain ...	Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein domain, shoulder, neck, and head, that form the phage tail base-plate. This entry represents the shoulder domain. This domain contains a beta sandwich fold [1].	Domain
A, B, C	PF08931	Lactophage receptor-binding protein C-terminal head domain (Caudo_bapla_RBP)	Lactophage receptor-binding protein C-terminal head domain	Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein domains, shoulders, neck, and head, that form the phage tail base-plate. In the overall structure this head domain exists as s ...	Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein domains, shoulders, neck, and head, that form the phage tail base-plate. In the overall structure this head domain exists as six trimers, and is necessary for specific recognition of the receptors at the host cell surface. Siphoviridae are the P2-like Caudovirales of Lactococcus [1]. This family now includes DUF1914. Family Baseplate, Pfam:PF16774, is the ORF15 or shoulder component of the base-plate complex.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	RECEPTOR BINDING PROTEIN	-	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell cell adhesion cellular process symbiont entry into host cell symbiont entry into host	virus tail virion component virus tail, baseplate

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR048779	Receptor binding protein, neck domain	Domain
A, B, C	IPR048780	Receptor-binding protein, N-terminal shoulder domain	Domain
A, B, C	IPR008982	Adenovirus pIV-like, attachment domain	Homologous Superfamily
A, B, C	IPR015027	Receptor-binding protein of phage tail base-plate Siphoviridae, head	Domain

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.