1QA9 | pdb_00001qa9

Structure of a Heterophilic Adhesion Complex Between the Human CD2 and CD58(LFA-3) Counter-Receptors

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)
B	d1qa9b_	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)
D	d1qa9d_	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	d1qa9a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD2, first domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1qa9c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD2, first 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)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054501	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054501	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054497	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054497	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)
B	V-set_9	e1qa9B1	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)
D	V-set_9	e1qa9D1	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)
A	V-set_15	e1qa9A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
C	V-set_15	e1qa9C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)
A	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)

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
B, D	Human CD58 protein	1V-LIKE	Homo sapiens (human)	CD58*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202546-0)
A, C	Human CD2 protein	1V-LIKE	Homo sapiens (human)	CD2*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202546-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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
B, D	HUMAN CD58 PROTEIN	protein binding binding signaling receptor binding	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 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 cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production response to peptide cellular response to tumor necrosis factor response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus cell adhesion cell-cell adhesion heterotypic cell-cell adhesion	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface ficolin-1-rich granule membrane ficolin-1-rich granule tertiary granule cell periphery plasma membrane
A, C	HUMAN CD2 PROTEIN	molecular transducer activity signaling receptor activity protein binding binding signaling receptor binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein kinase binding identical protein binding	response to stimulus immune response immune system process cellular process apoptotic process cell death programmed cell death multicellular organismal process regulation of leukocyte differentiation regulation of cellular process cellular developmental process regulation of developmental process regulation of leukocyte activation cell development response to stimulus immune response immune system process cellular process apoptotic process cell death programmed cell death multicellular organismal process regulation of leukocyte differentiation regulation of cellular process cellular developmental process regulation of developmental process regulation of leukocyte activation cell development regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte activation lymphocyte differentiation regulation of cell development leukocyte activation regulation of T cell differentiation multicellular organism development T cell activation cell differentiation anatomical structure development T cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of lymphocyte differentiation regulation of biological process regulation of multicellular organismal development hemopoiesis cell activation biological regulation regulation of T cell activation regulation of hemopoiesis leukocyte differentiation regulation of lymphocyte activation membrane organization cellular localization membrane raft polarization localization within membrane cellular component organization localization membrane raft localization membrane raft organization cellular component organization or biogenesis membrane raft distribution 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 response to external biotic stimulus natural killer cell mediated immunity cell killing 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 positive regulation of cellular process regulation of biosynthetic process 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 cellular response to stimulus cell surface receptor signaling pathway signaling signal transduction cell communication 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 myeloid dendritic cell activation positive regulation of myeloid dendritic cell activation myeloid leukocyte activation positive regulation of cell activation regulation of myeloid dendritic cell activation positive regulation of leukocyte activation positive regulation of immune system process	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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	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
A, C	Pharos: P06729	rheumatoid arthritis nephrotic syndrome psoriasis Sjogren syndrome thrombotic disease atypical teratoid rhabdoid tumor gastric cancer gout invasive ductal breast carcinoma lung carcinoma Malignant neoplasm of breast pilocytic astrocytoma subependymal giant cell astrocytoma cancer gastric carcinoma rheumatoid arthritis nephrotic syndrome psoriasis Sjogren syndrome thrombotic disease atypical teratoid rhabdoid tumor gastric cancer gout invasive ductal breast carcinoma lung carcinoma Malignant neoplasm of breast pilocytic astrocytoma subependymal giant cell astrocytoma cancer gastric carcinoma hematologic disease large cell medulloblastoma lymphatic system disease sarcoidosis ulcerative colitis cutaneous lupus erythematosus glioblastoma interstitial cystitis lung cancer malignant glioma osteosarcoma

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.