Annotations: 5B8C

High resolution structure of the human PD-1 in complex with pembrolizumab Fv

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
C	d5b8cc1	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)
C	d5b8cc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5b8cf1	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)
F	d5b8cf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5b8ci1	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)
I	d5b8ci2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d5b8cl1	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)
L	d5b8cl2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5b8cb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5b8ce_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5b8ch_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d5b8ck_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5b8ca_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5b8cd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5b8cg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5b8cj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	tRNA_anti-codon	e5b8cC1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
F	tRNA_anti-codon	e5b8cF1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
I	tRNA_anti-codon	e5b8cI1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
L	tRNA_anti-codon	e5b8cL1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
B	tRNA_anti-codon	e5b8cB1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
E	tRNA_anti-codon	e5b8cE1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
H	tRNA_anti-codon	e5b8cH1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
K	tRNA_anti-codon	e5b8cK1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
A	tRNA_anti-codon	e5b8cA1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
D	tRNA_anti-codon	e5b8cD1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
G	tRNA_anti-codon	e5b8cG1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)
J	tRNA_anti-codon	e5b8cJ1	A: alpha arrays	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: tRNA_anti-codon	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	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)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	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
C, F, I, L	PDCD1 (Programmed cell death protein 1)	1V-LIKE	Homo sapiens (human)	PDCD1*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202640-0)
B, E, H, K	Pembrolizumab	VH	Homo sapiens (human)	IGHV1-202, IGHJ401, IGHJ402, IGHJ403	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202640-0)
A, D, G, J	Pembrolizumab	V-KAPPA	Homo sapiens (human)	IGKV3D-1101, IGKJ401, IGKJ4*02	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202640-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E, H, K	Heavy Chain	IGHV1	-	programmed cell death protein 1	SAbDab (2026-10-16)
A, D, G, J	Light Chain	IGKV3	Kappa	programmed cell death protein 1	SAbDab (2026-10-16)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B, E, H, K	Pembrolizumab	PDCD1/CD279/PD1	Therapeutic SAbDab (2026-10-16)
A, D, G, J	Pembrolizumab	PDCD1/CD279/PD1	Therapeutic SAbDab (2026-10-16)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	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, F, I, L	Programmed cell death protein 1	molecular transducer activity signaling receptor activity transmembrane signaling receptor activity	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling negative regulation of signaling positive regulation of biological process negative regulation of biological process regulation of signal transduction regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication cell communication positive regulation of response to stimulus immune response-activating signaling pathway cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling negative regulation of signaling positive regulation of biological process negative regulation of biological process regulation of signal transduction regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response negative regulation of cellular process regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response negative regulation of response to stimulus biological regulation regulation of T cell receptor signaling pathway T cell receptor signaling pathway negative regulation of signal transduction negative regulation of T cell receptor signaling pathway regulation of response to stimulus negative regulation of immune system process immune system process regulation of immune response regulation of cell communication cellular process antigen receptor-mediated signaling pathway activation of immune response humoral immune response 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 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 T cell mediated immunity response to tumor cell regulation of adaptive immune response negative regulation of immune response negative regulation of immune effector process regulation of immune response to tumor cell negative regulation of adaptive immune response 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 negative regulation of leukocyte mediated immunity negative regulation of T cell mediated immunity apoptotic process cell death programmed cell death regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response multicellular organismal 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 regulation of multicellular organismal 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 multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane
B, E, H, K	Pembrolizumab heavy chain variable region (PemVH)	-	-	-
A, D, G, J	Pembrolizumab light chain variable region (PemVL)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, F, I, L	IPR042379	Programmed cell death protein 1	Family
C, F, I, L	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, F, I, L	IPR013106	Immunoglobulin V-set domain	Domain
C, F, I, L	IPR003599	Immunoglobulin domain subtype	Domain
C, F, I, L	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

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