2BSE

Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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	d2bsea_	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	(Lactococcus virus P2 ) [TaxId: 254252 ],	SCOPe (2.08)
B	d2bseb_	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	(Lactococcus virus P2 ) [TaxId: 254252 ],	SCOPe (2.08)
C	d2bsec_	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	(Lactococcus virus P2 ) [TaxId: 254252 ],	SCOPe (2.08)
D	d2bsed1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d2bsed2	Artifacts	Tags	Tags	Tags	N-terminal Tags	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d2bsee1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d2bsee2	Artifacts	Tags	Tags	Tags	N-terminal Tags	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d2bsef1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d2bsef2	Artifacts	Tags	Tags	Tags	N-terminal Tags	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Virus attachment protein globular domain	8036189	3001376	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Virus attachment protein globular domain	8036189	3001376	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Virus attachment protein globular domain	8036189	3001376	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_3rd	e2bseA1	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_3rd	e2bseB1	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_3rd	e2bseC1	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)
D	V-set_8	e2bseD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E	V-set_8	e2bseE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F	V-set_8	e2bseF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1830	Mainly Beta	Sandwich	Immunoglobulin-like	Phage tail base-plate Siphoviridae RBP, head domain	CATH (4.3.0)
B	2.60.40.1830	Mainly Beta	Sandwich	Immunoglobulin-like	Phage tail base-plate Siphoviridae RBP, head domain	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
D, E, F	Llama heavy chain VH domain	VH	Lama glama (llama)	IGHV3S301, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D, E, F	Heavy Chain	IGHV1	-	receptor binding protein	SAbDab (2024-04-19)

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	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	-	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell cell adhesion cellular process	virus tail virion component virus tail, baseplate
D, E, F	LLAMA IMMUNOGLOBULIN	-	-	-

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 National Science Foundation (DBI-1832184), 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 R01GM133198.