3BP5

Crystal structure of the mouse PD-1 and PD-L2 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT 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	d3bp5a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Programmed cell death protein 1, PD1, extracellular domain	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	V set domains-like	8054514	4007530	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054515	3000071	SCOP2 (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	I-set_6	e3bp5A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_6	ECOD (1.6)
B	I-set_8	e3bp5B4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	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
A	PDCD1 (PD-1, CD279), C50>S/B7DC (PD-L2, B7-DC) complex	1V-LIKE	Mus musculus (house mouse)	PDCD1*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE_1V-1C-LIKE	IMGT (202444-0)
B	PDCD1 (PD-1, CD279), C50>S/B7DC (PD-L2, B7-DC) complex	1V-1C-LIKE	Mus musculus (house mouse)	PDCD1LG2*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-LIKE_1V-1C-LIKE	IMGT (202444-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B	PF22705	Butyrophilin subfamily 3 member A2-like, Ig-C domain (C2-set_3)	Butyrophilin subfamily 3 member A2-like, Ig-C domain	This domain is found in human Butyrophilin subfamily 3 member A2 (BTN3A2), a protein that plays a role in T-cell responses in the adaptive immune response. BTN3A2 shows two extracellular domains: an N-terminal Ig-V like domain (Pfam:PF07686) and a C- ...	This domain is found in human Butyrophilin subfamily 3 member A2 (BTN3A2), a protein that plays a role in T-cell responses in the adaptive immune response. BTN3A2 shows two extracellular domains: an N-terminal Ig-V like domain (Pfam:PF07686) and a C-terminal Ig-C type domain that is located in the centre of the protein sequence [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Programmed cell death protein 1	molecular transducer activity signaling receptor activity	response to stimulus immune response immune system process adaptive immune response lymphocyte apoptotic process leukocyte apoptotic process B cell apoptotic process cellular process apoptotic process cell death programmed cell death regulation of biological process negative regulation of response to stimulus negative regulation of immune response response to stimulus immune response immune system process adaptive immune response lymphocyte apoptotic process leukocyte apoptotic process B cell apoptotic process cellular process apoptotic process cell death programmed cell death regulation of biological process negative regulation of response to stimulus negative regulation of immune response biological regulation negative regulation of biological process regulation of response to stimulus negative regulation of immune system process regulation of immune response regulation of immune system process immune system development developmental process multicellular organismal process regulation of developmental process negative regulation of developmental process multicellular organism development anatomical structure development negative regulation of tolerance induction regulation of multicellular organismal process regulation of tolerance induction negative regulation of multicellular organismal process tolerance induction system development T cell apoptotic process regulatory T cell apoptotic process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of cellular process positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of T cell apoptotic process regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process positive regulation of cellular process regulation of leukocyte activation regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte cell-cell adhesion negative regulation of cell adhesion leukocyte activation cell adhesion cell-cell adhesion T cell activation negative regulation of cellular process regulation of cell-cell adhesion regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of leukocyte activation regulation of lymphocyte activation regulation of B cell apoptotic process negative regulation of programmed cell death negative regulation of B cell apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process negative regulation of lymphocyte apoptotic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane
B	Programmed cell death 1 ligand 2	-	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication negative regulation of lymphocyte proliferation multicellular organismal process regulation of leukocyte activation negative regulation of biological process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication negative regulation of lymphocyte proliferation multicellular organismal process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of activated T cell proliferation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation activated T cell proliferation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of activated T cell proliferation negative regulation of immune system process immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation immune response adaptive immune response regulation of type II interferon production type II interferon production cellular biosynthetic process negative regulation of cellular metabolic process cytokine production regulation of cytokine production negative regulation of type II interferon production negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process positive regulation of biological process positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of immune system process positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion lymphocyte costimulation positive regulation of multicellular organismal process T cell costimulation biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin positive regulation of cell population proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of leukocyte proliferation positive regulation of mononuclear cell proliferation negative regulation of interleukin-10 production interleukin-10 production regulation of interleukin-10 production	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR042379	Programmed cell death protein 1	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR007110	Immunoglobulin-like domain	Domain
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR051713	T-cell Activation and Immune Regulation Protein	Family
B	IPR053896	Butyrophilin subfamily 3 member A2-like, Ig-C domain	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR003599	Immunoglobulin domain subtype	Domain
B	IPR007110	Immunoglobulin-like domain	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.