1CCZ | pdb_00001ccz

CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3) AT 1.8-A RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT 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	d1ccza1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD2-binding domain of CD58, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1ccza2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C2 set domains	CD2-binding domain of CD58, second 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)
A	SCOP2 Family	V set domains-like	8054500	4007530	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054501	3000071	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054745	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	C2-set	e1cczA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C2-set	ECOD (1.6)
A	V-set_9	e1cczA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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
A	Chimera of CD58 and CD2	1V-1C-LIKE	Homo sapiens (human)	CD58*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-1C-LIKE	IMGT (202512-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05790	Immunoglobulin C2-set domain (C2-set)	Immunoglobulin C2-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEIN (CD58)	protein binding binding signaling receptor binding kinase binding enzyme binding protein kinase binding protein tyrosine kinase binding receptor tyrosine kinase binding identical protein binding	response to stimulus immune response immune system process lymphocyte mediated immunity biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process defense response to other organism response to stress response to stimulus immune response immune system process lymphocyte mediated immunity biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process defense response to other organism response to stress natural killer cell mediated cytotoxicity innate immune response leukocyte mediated immunity cellular process response to external biotic stimulus natural killer cell mediated immunity cell killing multicellular organismal process regulation of cellular process positive regulation of interleukin-8 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation interleukin-8 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production T cell activation cell activation lymphocyte activation leukocyte activation natural killer cell activation cell adhesion cell-cell adhesion heterotypic cell-cell adhesion regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production regulation of type II interferon production type II interferon production positive regulation of type II interferon production response to peptide cellular response to tumor necrosis factor response to chemical response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor response to type II interferon cellular response to type II interferon	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex Golgi apparatus cytoplasm endomembrane system extracellular region cytoplasmic side of plasma membrane cytoplasmic side of membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle secretory granule secretory vesicle vesicle organelle membrane secretory granule membrane extracellular exosome extracellular vesicle extracellular organelle extracellular space extracellular membrane-bounded organelle ficolin-1-rich granule membrane ficolin-1-rich granule tertiary granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR015632	T-cell surface antigen CD2	Family
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR008424	Immunoglobulin C2-set	Domain
A	IPR015631	CD2/SLAM family receptor	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR015631	CD2/SLAM family receptor	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P19256	multiple sclerosis rheumatoid arthritis mature T-cell and NK-cell non-Hodgkin lymphoma pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma primitive neuroectodermal tumor Sjogren syndrome atypical teratoid rhabdoid tumor invasive ductal breast carcinoma lymphoplasmacytic lymphoma malignant mesothelioma medulloblastoma nephrosclerosis pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia multiple sclerosis rheumatoid arthritis mature T-cell and NK-cell non-Hodgkin lymphoma pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma primitive neuroectodermal tumor Sjogren syndrome atypical teratoid rhabdoid tumor invasive ductal breast carcinoma lymphoplasmacytic lymphoma malignant mesothelioma medulloblastoma nephrosclerosis pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pituitary cancer psoriasis subependymal giant cell astrocytoma Emery-Dreifuss muscular dystrophy large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Peripheral T-Cell Lymphoma primary biliary cholangitis tuberculosis glioblastoma lung carcinoma malignant glioma ovarian cancer

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.