8U31 | pdb_00008u31

Crystal structure of PD-1 in complex with a Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family 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)
A	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	Linocin_M18	e8u31C01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: Linocin_M18	ECOD (v294.1)
B	Linocin_M18	e8u31B01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: Linocin_M18	ECOD (v294.1)
A	Linocin_M18	e8u31A01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: Linocin_M18	ECOD (v294.1)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV3	-	programmed cell death protein 1	SAbDab (2026-03-27)
B	Light Chain	IGKV1	Kappa	programmed cell death protein 1	SAbDab (2026-03-27)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Fab heavy chain	-	-	-
B	Fab light chain	-	-	-
A	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 adaptive immune response humoral immune response lymphocyte apoptotic process leukocyte apoptotic process B cell apoptotic 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 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 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 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 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 positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process regulation of apoptotic 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 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 cellular anatomical structure cell surface membrane plasma membrane 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	IPR042379	Programmed cell death protein 1	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.