3KAA | pdb_00003kaa

Structure of Tim-3 in complex with phosphatidylserine

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3kaab_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3kaaa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	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	8083238	3000071	SCOP2B (2022-06-29)
A	SCOP2 Family	V set domains-like	8083237	4007530	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8083238	3000071	SCOP2 (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	Trypsin	e3kaaB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
A	NusG_II	e3kaaA1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: NusG_II	ECOD (v294.1)

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)
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, B	Hepatitis A virus cellular receptor 2	1V-LIKE	Mus musculus (house mouse)	TIMD3	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202611-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	Hepatitis A virus cellular receptor 2	cation binding ion binding binding metal ion binding small molecule binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of interleukin-1 production biological regulation 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 regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation negative regulation of natural killer cell activation leukocyte activation negative regulation of cellular process regulation of immune system process regulation of natural killer cell activation cell activation natural killer cell activation negative regulation of cell activation negative regulation of immune system process immune system process negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation cellular response to stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to stimulus response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response signal transduction positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of response to stimulus endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response defense response to symbiont negative regulation of type I interferon production negative regulation of macromolecule metabolic process type I interferon production negative regulation of metabolic process negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of type I interferon production regulation of tumor necrosis factor production negative regulation of tumor necrosis factor production tumor necrosis factor superfamily cytokine production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production regulation of macrophage colony-stimulating factor production negative regulation of macrophage colony-stimulating factor production regulation of granulocyte colony-stimulating factor production negative regulation of granulocyte colony-stimulating factor production granulocyte colony-stimulating factor production macrophage colony-stimulating factor production adaptive immune response interferon-alpha production regulation of interferon-alpha production negative regulation of interferon-alpha production negative regulation of interleukin-2 production regulation of interleukin-2 production interleukin-2 production interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production toll-like receptor 7 signaling pathway negative regulation of lymphocyte proliferation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation negative regulation of response to biotic stimulus defense response to bacterium response to bacterium regulation of defense response to bacterium negative regulation of response to stimulus negative regulation of defense response to bacterium negative regulation of response to external stimulus negative regulation of defense response macrophage activation involved in immune response cell activation involved in immune response myeloid cell activation involved in immune response myeloid leukocyte activation immune effector process macrophage activation leukocyte activation involved in immune response regulation of chemokine production chemokine production positive regulation of chemokine production lymphocyte mediated immunity regulation of immune effector process immune response to tumor cell negative regulation of immune response to tumor cell negative regulation of lymphocyte mediated immunity negative regulation of natural killer cell mediated immunity regulation of natural killer cell mediated cytotoxicity directed against tumor cell target leukocyte mediated immunity regulation of natural killer cell mediated immune response to tumor cell natural killer cell mediated immunity regulation of natural killer cell mediated immunity negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target negative regulation of immune response negative regulation of immune effector process leukocyte mediated cytotoxicity natural killer cell mediated immune response to tumor cell regulation of leukocyte mediated immunity natural killer cell mediated cytotoxicity regulation of cell killing negative regulation of natural killer cell mediated cytotoxicity regulation of natural killer cell mediated cytotoxicity negative regulation of response to tumor cell regulation of response to tumor cell negative regulation of leukocyte mediated cytotoxicity negative regulation of cell killing response to tumor cell regulation of leukocyte mediated cytotoxicity regulation of immune response to tumor cell natural killer cell mediated cytotoxicity directed against tumor cell target negative regulation of natural killer cell mediated immune response to tumor cell regulation of lymphocyte mediated immunity negative regulation of leukocyte mediated immunity cell killing negative regulation of innate immune response immunological synapse formation negative regulation of immunological synapse formation regulation of immunological synapse formation cell recognition cell-cell recognition positive regulation of defense response to bacterium regulation of type II interferon production type II interferon production negative regulation of type II interferon production immune system development developmental process multicellular organism development natural killer cell tolerance induction anatomical structure development tolerance induction system development toll-like receptor 3 signaling pathway positive regulation of cell population proliferation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation positive regulation of cell adhesion regulation of macrophage activation positive regulation of macrophage activation positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling multi-multicellular organism process maternal process involved in female pregnancy reproductive process multicellular organismal reproductive process female pregnancy multi-organism reproductive process response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to chemical stimulus response to chemical cellular response to lipid response to molecule of bacterial origin myeloid dendritic cell activation negative regulation of myeloid dendritic cell activation regulation of myeloid dendritic cell activation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains negative regulation of T-helper 1 type immune response regulation of adaptive immune response negative regulation of adaptive immune response T-helper 1 type immune response regulation of T-helper 1 type immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains tolerance induction dependent upon immune response regulation of tolerance induction dependent upon immune response regulation of tolerance induction negative regulation of interleukin-3 production interleukin-3 production regulation of interleukin-3 production T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell T cell activation involved in immune response lymphocyte activation involved in immune response regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction inflammatory response RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of type II interferon production defense response to Gram-positive bacterium	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle mediator complex cell surface anchoring junction cell junction cell periphery membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle mediator complex cell surface anchoring junction cell junction cell periphery plasma membrane membrane early endosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle cytoplasm vesicle immunological synapse extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR051669	Immune Modulating & Transcription Coactivator	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Bitopic proteins	Immunoglobulin superfamily	T-cell immunoglobulin and mucin domain-containing (TIM) protein

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.