8GY5

High-resolution structure of the cemiplimab Fab in complex with PD-1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth Q]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8059477	3000071	SCOP2B (2022-06-29)
F [auth P]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8059477	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	PF07654	e8gy5A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF07686	e8gy5A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth H]	PF07654	e8gy5H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth H]	PF07686	e8gy5H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF07654	e8gy5B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07686	e8gy5B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth L]	PF07654	e8gy5L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth L]	PF07686	e8gy5L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth Q]	PF07686	e8gy5Q1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth P]	PF07686	e8gy5P1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth H]	Heavy Chain	IGHV3	-	programmed cell death protein 1	SAbDab (2024-05-10)
B, E [auth L]	Light Chain	IGKV1	Kappa	programmed cell death protein 1	SAbDab (2024-05-10)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A, D [auth H]	Cemiplimab	PDCD1/CD279/PD1	Therapeutic SAbDab (2024-05-10)
B, E [auth L]	Cemiplimab	PDCD1/CD279/PD1	Therapeutic SAbDab (2024-05-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth H]	heavy chain	-	-	-
B, E [auth L]	light chain	-	-	-
C [auth Q], F [auth P]	Programmed cell death protein 1	-	response to stimulus immune response immune system process adaptive immune response humoral 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 response to stimulus immune response immune system process adaptive immune response humoral 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
C [auth Q], F [auth P]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth Q], F [auth P]	IPR003599	Immunoglobulin subtype	Domain
C [auth Q], F [auth P]	IPR042379	Programmed cell death protein 1	Family
C [auth Q], F [auth P]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth Q], F [auth P]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth Q], F [auth P]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth Q], F [auth P]	Pharos: Q15116	melanoma systemic lupus erythematosus lymphatic system disease Malignant tumor of head and/or neck multiple sclerosis, susceptibility to 1 allergic rhinitis psoriasis brain aneurysm squamous cell lung carcinoma cancer transitional cell carcinoma Crohn disease esophageal squamous cell carcinoma hematologic disease lung disease melanoma systemic lupus erythematosus lymphatic system disease Malignant tumor of head and/or neck multiple sclerosis, susceptibility to 1 allergic rhinitis psoriasis brain aneurysm squamous cell lung carcinoma cancer transitional cell carcinoma Crohn disease esophageal squamous cell carcinoma hematologic disease lung disease malignant pleural mesothelioma non-small cell lung carcinoma asthma skin disease brain glioma cutaneous melanoma gastric cancer kidney disease lupus erythematosus multiple sclerosis ovarian cancer autoimmune disease squamous cell carcinoma breast disease systemic lupus erythematosus, susceptibility to, 2 connective tissue disease endometrial carcinoma head and neck cancer liver disease

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 R01GM133198.