5WT9

Complex structure of PD-1 and nivolumab-Fab

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth H]	d5wt9h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5wt9l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5wt9l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth G]	d5wt9g_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Programmed cell death protein 1, PD1, extracellular domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth G]	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 [auth H]	PF07654	e5wt9H2	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 [auth H]	PF07686	e5wt9H1	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 [auth L]	PF07654	e5wt9L2	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 [auth L]	PF07686	e5wt9L1	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 G]	PF07686	e5wt9G1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV3	-	programmed cell death protein 1	SAbDab (2024-04-26)
B [auth L]	Light Chain	IGKV3	Kappa	programmed cell death protein 1	SAbDab (2024-04-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth H]	Nivolumab	PDCD1/CD279/PD1	Therapeutic SAbDab (2024-04-26)
B [auth L]	Nivolumab	PDCD1/CD279/PD1	Therapeutic SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth G]	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 [auth H]	Heavy Chain of Nivolumab	-	-	-
B [auth L]	Light Chain of Nivolumab	-	-	-
C [auth G]	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 G]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth G]	IPR003599	Immunoglobulin subtype	Domain
C [auth G]	IPR042379	Programmed cell death protein 1	Family
C [auth G]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth G]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth G]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth G]	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 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.