6J15

Complex structure of GY-5 Fab and PD-1

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth H]	d6j15h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth H]	d6j15h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth A]	d6j15a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth A]	d6j15a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d6j15l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d6j15l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d6j15b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d6j15b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth C]	d6j15c1	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)
A [auth C]	d6j15c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth D]	d6j15d1	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)
B [auth D]	d6j15d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A [auth C]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8059477	3000071	SCOP2B (2022-06-29)
B [auth D]	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)
C [auth H]	C1-set_1	e6j15H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth H]	V-set_10	e6j15H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
E [auth A]	C1-set_1	e6j15A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth A]	V-set_10	e6j15A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
D [auth L]	C1-set_4	e6j15L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth L]	V-set	e6j15L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F [auth B]	C1-set_4	e6j15B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
F [auth B]	V-set	e6j15B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
A [auth C]	V-set_4	e6j15C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_4	ECOD (1.6)
B [auth D]	V-set_4	e6j15D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

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
C [auth H], E [auth A]	mAb GY-5, anti-PDCD1-1	VH-CH1	Mus musculus (house mouse)	IGHV1S13701, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)
D [auth L], F [auth B]	mAb GY-5, anti-PDCD1-1	L-KAPPA	Mus musculus (house mouse)	IGKV1-11701, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)
A [auth C], B [auth D]	Programmed cell death protein 1	1V-LIKE	Homo sapiens (human)	PDCD1*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], E [auth A]	Heavy Chain	IGHV1	-	programmed cell death protein 1	SAbDab (2024-10-25)
D [auth L], F [auth B]	Light Chain	IGKV1	Kappa	programmed cell death protein 1	SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth D]	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
C [auth H], E [auth A]	GY-5 heavy chain Fab	-	-	-
D [auth L], F [auth B]	GY-5 light chain Fab	-	-	-
A [auth C], B [auth D]	Programmed cell death protein 1	molecular transducer activity signaling receptor activity	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 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity 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 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity regulation of response to biotic stimulus negative regulation of response to biotic stimulus immune response to tumor cell negative regulation of biological process negative regulation of immune response to tumor cell negative regulation of response to tumor cell negative regulation of lymphocyte mediated immunity regulation of response to tumor cell response to biotic stimulus T cell mediated immune response to tumor cell negative regulation of T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell leukocyte mediated immunity regulation of immune system process regulation of T cell mediated immunity response to tumor cell regulation of biological process regulation of adaptive immune response negative regulation of response to stimulus negative regulation of immune response biological regulation negative regulation of immune effector process regulation of immune response to tumor cell negative regulation of adaptive immune response immune effector process negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of response to stimulus negative regulation of immune system process regulation of immune response negative regulation of leukocyte mediated immunity negative regulation of T cell mediated immunity 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], B [auth D]	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 R01GM157729.