3HCS | pdb_00003hcs

Crystal structure of the N-terminal domain of TRAF6

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8053196	3001077	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RING/U-box like	8053202	3000160	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8053197	3001077	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8053198	3001077	SCOP2B (2022-06-29)
A	SCOP2 Family	TRAF-type zinc finger	8049971	4006710	SCOP2 (2022-06-29)
A	SCOP2 Family	RING finger domain, C3HC4	8053200	4000374	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-beta-alpha zinc fingers	8053196	3001077	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RING/U-box like	8053202	3000160	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-beta-alpha zinc fingers	8053197	3001077	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-beta-alpha zinc fingers	8053198	3001077	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	AAA_31	e3hcsB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: AAA_31	ECOD (v294.1)
A	zf-C3HC4_2	e3hcsA1	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: zf-C3HC4_2	ECOD (v294.1)
A	TRAF6_Z2	e3hcsA3	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: TRAF6_Z2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13923	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)	Zinc finger, C3HC4 type (RING finger)		Domain
A, B	PF18048	TNF receptor-associated factor 6 zinc finger 2 (TRAF6_Z2)	TNF receptor-associated factor 6 zinc finger 2	This domain is the second of three zinc fingers of Homo sapiens TNF receptor associated factor 6 (TRAF6). TRAF6 mediates Lys63 (K63)-linked polyubiquitination for Necrosis Factor-kappaB activation. The first three residues and the last Cys of finger ...	This domain is the second of three zinc fingers of Homo sapiens TNF receptor associated factor 6 (TRAF6). TRAF6 mediates Lys63 (K63)-linked polyubiquitination for Necrosis Factor-kappaB activation. The first three residues and the last Cys of finger 1 form a classical type I beta-turn [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	TNF receptor-associated factor 6	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding binding protein kinase B binding kinase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding binding protein kinase B binding kinase binding enzyme binding protein kinase binding histone deacetylase binding protein-macromolecule adaptor activity molecular adaptor activity identical protein binding signaling adaptor activity ubiquitin-like protein conjugating enzyme binding ubiquitin conjugating enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus intracellular signal transduction cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus intracellular signal transduction cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response cellular process activation of immune response cellular response to stress DNA damage response toll-like receptor signaling pathway MyD88-dependent toll-like receptor signaling pathway adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process cytokine production leukocyte mediated immunity positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity regulation of T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of lymphocyte mediated immunity positive regulation of gene expression positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cell surface receptor signaling pathway interleukin-33-mediated signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide response to chemical cellular response to cytokine stimulus protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to interleukin-17 response to interleukin-17 interleukin-17-mediated signaling pathway non-canonical NF-kappaB signal transduction intracellular signaling cassette regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of molecular function positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of protein kinase activity phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity regulation of protein kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity regulation of phosphorylation regulation of phosphorus metabolic process developmental process multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development CD40 signaling pathway embryonic epithelial tube formation tube formation epithelial tube formation tube morphogenesis primary neural tube formation epithelial tube morphogenesis system development morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication positive regulation of signaling protein polyubiquitination regulation of lipopolysaccharide-mediated signaling pathway response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to bacterium response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to lipid positive regulation of lipopolysaccharide-mediated signaling pathway response to molecule of bacterial origin immune response-regulating cell surface receptor signaling pathway Fc receptor signaling pathway Fc-epsilon receptor signaling pathway ossification cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of MAP kinase activity positive regulation of JUN kinase activity regulation of protein serine/threonine kinase activity regulation of JUN kinase activity negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process endolysosomal toll-like receptor signaling pathway toll-like receptor 3 signaling pathway positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of type I interferon production type I interferon production regulation of type I interferon production positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process multicellular organismal-level homeostasis homeostatic process tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption interleukin-17A-mediated signaling pathway positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction protein branched polyubiquitination immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway myeloid leukocyte differentiation cellular developmental process myeloid dendritic cell activation hemopoiesis cell development mononuclear cell differentiation myeloid leukocyte activation myeloid cell differentiation cell differentiation myeloid dendritic cell differentiation dendritic cell differentiation leukocyte differentiation cell surface toll-like receptor signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway odontogenesis of dentin-containing tooth odontogenesis animal organ development animal organ morphogenesis autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis process utilizing autophagic mechanism interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production response to interleukin-1 antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification response to lectin cellular response to lectin stimulatory C-type lectin receptor signaling pathway regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway regulation of localization cellular localization protein localization to synapse regulation of protein localization regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane localization intracellular protein localization regulation of biological quality regulation of protein localization to membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to cell periphery protein localization to postsynaptic membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane protein-containing complex localization regulation of postsynaptic membrane neurotransmitter receptor levels regulation of cellular localization macromolecule localization protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse protein K63-linked ubiquitination defense response to virus antiviral innate immune response response to virus immunoglobulin production regulation of immunoglobulin production regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production T-helper 1 type immune response osteoclast differentiation cellular response to interleukin-1 interleukin-1-mediated signaling pathway positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte adhesion to vascular endothelial cell leukocyte adhesion to vascular endothelial cell regulation of leukocyte differentiation regulation of developmental process regulation of cell differentiation positive regulation of osteoclast differentiation regulation of cell development positive regulation of developmental process regulation of osteoclast differentiation positive regulation of cell differentiation positive regulation of hemopoiesis regulation of multicellular organismal development regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex signaling receptor complex CD40 receptor complex intracellular anatomical structure cytoplasm cytosol synapse cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex signaling receptor complex CD40 receptor complex intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse extrinsic component of plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane side of membrane perinuclear region of cytoplasm endosome membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle vesicle organelle membrane cell cortex lipid droplet membraneless organelle intracellular membraneless organelle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012227	TNF receptor-associated factor TRAF, metazoa	Family
A, B	IPR001293	Zinc finger, TRAF-type	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR027139	TNF receptor-associated factor 6, C3HC3D-type RING zinc finger	Domain
A, B	IPR001841	Zinc finger, RING-type	Domain
A, B	IPR008974	TRAF-like	Homologous Superfamily
A, B	IPR037309	TNF receptor-associated factor 6, MATH domain	Domain
A, B	IPR002083	MATH/TRAF domain	Domain
A, B	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B	IPR049342	TRAF1-6, MATH domain	Domain
A, B	IPR041310	TNF receptor-associated factor 6, zinc finger 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y4K3	rheumatoid arthritis coronary artery disease acute myeloid leukemia Autosomal dominant hypohidrotic ectodermal dysplasia syndrome (disorder) atopic eczema autoimmune 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.