2PKD | pdb_00002pkd

Crystal structure of CD84: Insite into SLAM family function

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	DAO, NAD_binding_8	e2pkdF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
E	DAO, NAD_binding_8	e2pkdE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
D	DAO, NAD_binding_8	e2pkdD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
C	DAO, NAD_binding_8	e2pkdC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
B	DAO, NAD_binding_8	e2pkdB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
A	Asp_Glu_race	e2pkdA1	A: a/b three-layered sandwiches	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Asp_Glu_race	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	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)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	SLAM family member 5	identical protein binding protein binding binding	multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation regulation of cellular process negative regulation of biological process regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation regulation of cellular process negative regulation of biological process regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression regulation of interleukin-18 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of interleukin-18 production negative regulation of multicellular organismal process regulation of metabolic process interleukin-18 production regulation of store-operated calcium entry regulation of calcium ion transport regulation of localization transport regulation of transport regulation of monoatomic ion transport establishment of localization calcium ion transport metal ion transport localization store-operated calcium entry monoatomic ion transport monoatomic cation transport regulation of metal ion transport response to stimulus immune response adaptive immune response establishment of organelle localization regulation of immune effector process regulation of myeloid leukocyte mediated immunity regulated exocytosis negative regulation of transport cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity vesicle-mediated transport myeloid leukocyte activation negative regulation of secretion establishment of localization in cell leukocyte mediated immunity regulation of immune system process negative regulation of secretion by cell negative regulation of myeloid leukocyte mediated immunity negative regulation of immune effector process vacuolar localization mast cell degranulation immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis lysosome localization cellular localization negative regulation of regulated secretory pathway negative regulation of leukocyte degranulation regulation of mast cell degranulation regulation of regulated secretory pathway secretion by cell regulation of secretion by cell negative regulation of exocytosis organelle localization leukocyte activation involved in immune response negative regulation of mast cell degranulation mast cell activation regulation of leukocyte degranulation mast cell mediated immunity secretion export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response mast cell activation involved in immune response negative regulation of immune system process regulation of exocytosis negative regulation of leukocyte mediated immunity granulocyte macrophage colony-stimulating factor production regulation of primary metabolic process negative regulation of granulocyte macrophage colony-stimulating factor production protein metabolic process negative regulation of protein metabolic process regulation of granulocyte macrophage colony-stimulating factor production regulation of protein metabolic process primary metabolic process catabolic process autophagy process utilizing autophagic mechanism cell adhesion cell-cell adhesion homophilic cell-cell adhesion biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of leukocyte activation regulation of cell activation negative regulation of cell activation negative regulation of mast cell activation regulation of mast cell activation negative regulation of leukocyte activation	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, B, C, D, E A, B, C, D, E, F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR015631	CD2/SLAM family receptor	Family
A, B, C, D, E A, B, C, D, E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003599	Immunoglobulin domain subtype	Domain
A, B, C, D, E A, B, C, D, E, F	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q9UIB8	pilocytic astrocytoma Sjogren syndrome ulcerative colitis Abortion, Spontaneous B-cell chronic lymphocytic leukemia glioblastoma interstitial cystitis lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis chronic obstructive pulmonary disease Graves disease invasive ductal breast carcinoma lung carcinoma pilocytic astrocytoma Sjogren syndrome ulcerative colitis Abortion, Spontaneous B-cell chronic lymphocytic leukemia glioblastoma interstitial cystitis lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis chronic obstructive pulmonary disease Graves disease invasive ductal breast carcinoma lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sarcoidosis subependymal giant cell astrocytoma astrocytic tumor cutaneous lupus erythematosus head and neck cancer large cell medulloblastoma malignant glioma pancreatic intraductal papillary-mucinous carcinoma

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.