3BIK

Crystal Structure of the PD-1/PD-L1 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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3bikb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Programmed cell death protein 1, PD1, extracellular domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3bikc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Programmed cell death protein 1, PD1, extracellular domain	house 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)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054515	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054515	3000071	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	I-set_8	e3bikA2	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)
B	I-set_6	e3bikB1	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)
C	I-set_6	e3bikC1	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)

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)
C	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	CD274 (PDL1, B7H1, PDCD1L1)	1V-1C-LIKE	Homo sapiens (human)	CD274*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-1C-LIKE	IMGT (202415-0)
B, C	PDCD1 (PD1, CD279)	1V-LIKE	Mus musculus (house mouse)	PDCD1*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202415-0)

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
A	PF08205	CD80-like C2-set immunoglobulin domain (C2-set_2)	CD80-like C2-set immunoglobulin domain	These domains belong to the immunoglobulin superfamily.	Domain
B, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Programmed cell death 1 ligand 1	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process leukocyte apoptotic process positive regulation of biological process regulation of programmed cell death lymphocyte apoptotic process regulation of activated CD8-positive, alpha-beta T cell apoptotic process activated CD8-positive, alpha-beta T cell apoptotic process regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process positive regulation of cellular process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of biological process positive regulation of programmed cell death regulation of cellular process leukocyte apoptotic process positive regulation of biological process regulation of programmed cell death lymphocyte apoptotic process regulation of activated CD8-positive, alpha-beta T cell apoptotic process activated CD8-positive, alpha-beta T cell apoptotic process regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process positive regulation of cellular process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of biological process positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process positive regulation of T cell apoptotic process positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process cellular process T cell apoptotic process apoptotic process programmed cell death 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 response to stimulus immune response adaptive immune response cellular response to stimulus response to organic substance 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 cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus pattern recognition receptor signaling pathway regulation of response to external stimulus toll-like receptor signaling pathway signaling cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response defense response regulation of innate immune response defense response to symbiont TRIF-dependent toll-like receptor signaling pathway regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response MyD88-independent toll-like receptor signaling pathway activation of immune response response to cytokine negative regulation of interleukin-10 production cellular biosynthetic process interleukin-10 production negative regulation of cellular metabolic process organic substance metabolic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of interleukin-10 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 regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cell surface receptor signaling pathway tumor necrosis factor superfamily cytokine production regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of interleukin-10 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of type II interferon production type II interferon production negative regulation of type II interferon production 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 T cell activation positive regulation of cell adhesion lymphocyte costimulation T cell costimulation regulation of alpha-beta T cell activation alpha-beta T cell proliferation alpha-beta T cell activation regulation of CD4-positive, alpha-beta T cell proliferation negative regulation of CD4-positive, alpha-beta T cell activation regulation of alpha-beta T cell proliferation CD4-positive, alpha-beta T cell activation CD4-positive, alpha-beta T cell proliferation negative regulation of alpha-beta T cell proliferation regulation of CD4-positive, alpha-beta T cell activation negative regulation of CD4-positive, alpha-beta T cell proliferation negative regulation of alpha-beta T cell activation 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 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains immune response to tumor cell positive regulation of peripheral tolerance induction multicellular organism development anatomical structure development regulation of peripheral tolerance induction positive regulation of adaptive immune response system development developmental process tolerance induction dependent upon immune response positive regulation of tolerance induction dependent upon immune response positive regulation of immune response to tumor cell regulation of adaptive immune response regulation of tolerance induction dependent upon immune response peripheral tolerance induction positive regulation of tolerance induction tolerance induction positive regulation of response to tumor cell immune system development positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains tolerance induction to tumor cell regulation of tolerance induction to tumor cell response to tumor cell regulation of immune response to tumor cell regulation of tolerance induction positive regulation of tolerance induction to tumor cell CD8-positive, alpha-beta T cell activation negative regulation of CD8-positive, alpha-beta T cell activation regulation of CD8-positive, alpha-beta T cell activation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome membrane endosome intracellular vesicle recycling endosome endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane cytoplasmic vesicle cytoplasm organelle membrane early endosome early endosome membrane
B, C	Programmed cell death protein 1	-	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 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 cellular 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR003599	Immunoglobulin subtype	Domain
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A	IPR007110	Immunoglobulin-like domain	Domain
B, C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, C	IPR003599	Immunoglobulin subtype	Domain
B, C	IPR042379	Programmed cell death protein 1	Family
B, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, C	IPR013106	Immunoglobulin V-set domain	Domain
B, C	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NZQ7	thymus cancer lymphoma non-small cell lung carcinoma allergic disease hepatocellular carcinoma cancer Neoplasms, Radiation-Induced pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia drug dependence prostate disease head and neck cancer skin disease substance abuse interstitial cystitis atopic eczema thymus cancer lymphoma non-small cell lung carcinoma allergic disease hepatocellular carcinoma cancer Neoplasms, Radiation-Induced pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia drug dependence prostate disease head and neck cancer skin disease substance abuse interstitial cystitis atopic eczema liver disease breast cancer lung disease transitional cell carcinoma urinary bladder disease congestive heart failure cystic fibrosis osteosarcoma polycystic ovary syndrome psoriasis renal cell carcinoma hematologic disease small cell lung carcinoma kidney disease substance-related disorder autoimmune disease lung benign neoplasm thymus neoplasm breast disease tuberculosis chronic obstructive pulmonary disease uterine disease connective tissue disease nasopharyngeal carcinoma oligodendroglioma diffuse large B-cell lymphoma ovarian disease Hashimoto thyroiditis sarcoidosis stomach disease hypothyroidism substance dependence asthma brain disease lung carcinoma trabecular adenocarcinoma lymphatic system disease ulcerative colitis colonic disease medulloblastoma Crohn disease

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.