Annotations: 8WRY

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 Complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	WD40	e8wryC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B [auth D]	WD40	e8wryD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C [auth B]	WD40	e8wryB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
D [auth A]	WD40	e8wryA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], D [auth A]	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	Lymphocyte antigen 96	Toll-like receptor 4 binding protein binding binding signaling receptor binding Toll-like receptor binding molecular transducer activity pattern recognition receptor activity signaling receptor activity lipopolysaccharide immune receptor activity lipid binding lipopolysaccharide binding carbohydrate derivative binding	biological process involved in interspecies interaction between organisms response to stimulus detection of external biotic stimulus response to lipid response to other organism detection of lipopolysaccharide response to oxygen-containing compound response to external stimulus detection of molecule of bacterial origin detection of biotic stimulus response to lipopolysaccharide response to biotic stimulus detection of stimulus response to bacterium response to chemical biological process involved in interspecies interaction between organisms response to stimulus detection of external biotic stimulus response to lipid response to other organism detection of lipopolysaccharide response to oxygen-containing compound response to external stimulus detection of molecule of bacterial origin detection of biotic stimulus response to lipopolysaccharide response to biotic stimulus detection of stimulus response to bacterium response to chemical detection of chemical stimulus response to external biotic stimulus response to molecule of bacterial origin cellular response to stimulus positive regulation of cell communication regulation of lipopolysaccharide-mediated signaling pathway positive regulation of response to biotic stimulus regulation of response to biotic stimulus regulation of cellular process positive regulation of signal transduction regulation of response to external stimulus signaling cellular response to lipopolysaccharide positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus positive regulation of response to external stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to chemical stimulus regulation of response to stimulus cellular response to lipid regulation of cell communication cellular process positive regulation of lipopolysaccharide-mediated signaling pathway positive regulation of signaling immune response-regulating cell surface receptor signaling pathway pattern recognition receptor signaling pathway immune response-activating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface toll-like receptor signaling pathway innate immune response-activating signaling pathway immune response immune response-activating cell surface receptor signaling pathway regulation of innate immune response defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response innate immune response activating cell surface receptor signaling pathway immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response cell surface pattern recognition receptor signaling pathway positive regulation of innate immune response defense response defense response to symbiont immune system process toll-like receptor 4 signaling pathway inflammatory response multicellular organismal process regulation of tumor necrosis factor production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of biosynthetic process tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production 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 toll-like receptor signaling pathway	protein-containing complex signaling receptor complex cellular anatomical structure extracellular region cell periphery plasma membrane membrane lipopolysaccharide receptor complex membrane protein complex
C [auth B], D [auth A]	Toll-like receptor 4	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding binding signaling receptor binding lipid binding lipopolysaccharide binding carbohydrate derivative binding pattern recognition receptor activity lipopolysaccharide immune receptor activity phosphatidylinositol 3-kinase binding identical protein binding protein heterodimerization activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding binding signaling receptor binding lipid binding lipopolysaccharide binding carbohydrate derivative binding pattern recognition receptor activity lipopolysaccharide immune receptor activity phosphatidylinositol 3-kinase binding identical protein binding protein heterodimerization activity protein dimerization activity	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process multicellular organismal process interleukin-1 production positive regulation of macromolecule 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 regulation of interleukin-1 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of tumor necrosis factor production negative regulation of biological process negative regulation of tumor necrosis factor production negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production tumor necrosis factor production negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process growth plate cartilage morphogenesis growth animal organ development tissue development anatomical structure morphogenesis tissue morphogenesis bone growth cartilage morphogenesis skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis cartilage development cellular response to stimulus cellular response to low-density lipoprotein particle stimulus cellular response to oxidised low-density lipoprotein particle stimulus response to stimulus response to endogenous stimulus response to chemical response to lipoprotein particle cellular response to lipoprotein particle stimulus interleukin-13 production positive regulation of interleukin-13 production regulation of interleukin-13 production regulation of localization establishment of protein localization regulation of protein localization transport matrix metallopeptidase secretion positive regulation of matrix metallopeptidase secretion positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization secretion by cell regulation of secretion by cell positive regulation of secretion intracellular protein localization regulation of matrix metallopeptidase secretion secretion regulation of transport establishment of protein localization to extracellular region regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus regulation of response to external stimulus 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 innate immune response regulation of immune system process positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response immune response regulation of innate immune response defense response to symbiont immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response positive regulation of cell communication positive regulation of signal transduction pattern recognition receptor signaling pathway positive regulation of pattern recognition receptor signaling pathway positive regulation of intracellular signal transduction positive regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway regulation of pattern recognition receptor signaling pathway regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway nucleotide-binding oligomerization domain containing 2 signaling pathway regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway positive regulation of signaling positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process phosphate-containing compound metabolic process protein modification process positive regulation of protein phosphorylation activation of NF-kappaB-inducing kinase activity protein phosphorylation phosphorylation non-canonical NF-kappaB signal transduction regulation of protein metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation detection of external stimulus system process nervous system process sensory perception of temperature stimulus sensory perception of pain detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of temperature stimulus response to abiotic stimulus detection of stimulus involved in sensory perception detection of temperature stimulus involved in sensory perception of pain regulation of chemokine production chemokine production positive regulation of chemokine production signal transduction involved in regulation of gene expression cellular response to lipoteichoic acid response to oxygen-containing compound response to lipoteichoic acid cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to chemical stimulus response to molecule of bacterial origin interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation regulation of type II interferon production type II interferon production negative regulation of type II interferon production defense response to Gram-negative bacterium regulation of immune effector process positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response regulation of cytokine production involved in immune response immune effector process regulation of macrophage cytokine production positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of macrophage cytokine production macrophage cytokine production epithelial structure maintenance homeostatic process digestive system process intestinal epithelial structure maintenance tissue homeostasis maintenance of gastrointestinal epithelium digestion multicellular organismal-level homeostasis anatomical structure homeostasis interleukin-17 production negative regulation of interleukin-17 production regulation of interleukin-17 production B cell proliferation involved in immune response B cell activation cell activation B cell proliferation B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte proliferation leukocyte activation mononuclear cell proliferation leukocyte activation involved in immune response lymphocyte proliferation lymphocyte activation involved in immune response icosanoid metabolic process leukotriene metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process myeloid leukocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation inflammatory response glial cell activation neuroinflammatory response interferon-alpha production regulation of interferon-alpha production positive regulation of type I interferon production type I interferon production positive regulation of interferon-alpha production regulation of type I interferon production positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction regulation of macrophage activation positive regulation of macrophage activation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation positive regulation of leukocyte activation detection of mechanical stimulus involved in sensory perception of pain response to mechanical stimulus detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of mechanical stimulus neurogenesis cellular developmental process cell differentiation nervous system development T cell activation alpha-beta T cell activation NK T cell activation positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death cell surface receptor signaling pathway regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway cell death positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production toll-like receptor signaling pathway TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production myeloid leukocyte differentiation hemopoiesis macrophage differentiation cell development mononuclear cell differentiation central nervous system development gliogenesis glial cell differentiation myeloid cell differentiation microglia differentiation leukocyte differentiation regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly cellular component biogenesis cellular component assembly inflammasome-mediated signaling pathway canonical inflammasome complex assembly positive regulation of inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway NLRP3 inflammasome complex assembly regulation of cellular component organization positive regulation of cellular component organization cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis response to type II interferon response to cytokine cellular response to type II interferon response to peptide cellular response to cytokine stimulus mast cell activation cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus reactive oxygen species biosynthetic process positive regulation of reactive oxygen species biosynthetic process reactive oxygen species metabolic process regulation of reactive oxygen species biosynthetic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process regulation of MHC class II biosynthetic process MHC class II biosynthetic process positive regulation of MHC class II biosynthetic process regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response response to lipid response to fatty acid regulation of body fluid levels positive regulation of platelet activation coagulation regulation of biological quality response to wounding wound healing hemostasis blood coagulation regulation of platelet activation platelet activation immune response-regulating cell surface receptor signaling pathway cell surface toll-like receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of toll-like receptor 4 signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production response to oxidative stress negative regulation of cold-induced thermogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis cellular response to nitrogen compound response to nitrogen compound cellular response to amyloid-beta response to amyloid-beta response to lipopolysaccharide positive regulation of type II interferon production regulation of cellular response to stress stress-activated MAPK cascade cellular response to stress positive regulation of stress-activated protein kinase signaling cascade positive regulation of stress-activated MAPK cascade regulation of stress-activated protein kinase signaling cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade MyD88-dependent toll-like receptor signaling pathway regulation of inflammatory response positive regulation of inflammatory response interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production import into cell phagocytosis endocytosis vesicle-mediated transport interleukin-23 production regulation of interleukin-23 production negative regulation of interleukin-23 production astrocyte differentiation glial cell development astrocyte development regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production chemokine (C-X-C motif) ligand 2 production regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of JNK cascade JNK cascade regulation of JNK cascade wound healing involved in inflammatory response inflammatory response to wounding nitric oxide production involved in inflammatory response positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway nucleotide-binding oligomerization domain containing 1 signaling pathway regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway positive regulation of B cell proliferation regulation of B cell proliferation regulation of B cell activation positive regulation of B cell activation positive regulation of DNA-templated transcription RNA 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 positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription detection of external biotic stimulus detection of lipopolysaccharide detection of molecule of bacterial origin detection of biotic stimulus detection of chemical stimulus cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to platelet-derived growth factor stimulus response to growth factor response to platelet-derived growth factor positive regulation of interleukin-6 production cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to lipid response to alcohol response to ethanol dendritic cell cytokine production regulation of dendritic cell cytokine production leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of response to macrophage colony-stimulating factor response to macrophage colony-stimulating factor positive regulation of response to cytokine stimulus cellular response to macrophage colony-stimulating factor stimulus regulation of response to cytokine stimulus regulation of cellular response to macrophage colony-stimulating factor stimulus positive regulation of response to macrophage colony-stimulating factor positive regulation of cellular response to macrophage colony-stimulating factor stimulus negative regulation of cytokine production involved in inflammatory response	protein-containing complex signaling receptor complex endosome membrane membrane-bounded organelle intracellular anatomical structure membrane endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle protein-containing complex signaling receptor complex endosome membrane membrane-bounded organelle intracellular anatomical structure membrane endosome 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 cytoplasm vesicle organelle membrane phagocytic cup cell periphery plasma membrane cell surface external side of plasma membrane side of membrane ruffle cell projection cell leading edge plasma membrane bounded cell projection perinuclear region of cytoplasm lipopolysaccharide receptor complex membrane protein complex early endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth D]	IPR003172	MD-2-related lipid-recognition domain	Domain
A [auth C], B [auth D]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth C], B [auth D]	IPR039217	Lymphocyte antigen 96	Family
C [auth B], D [auth A]	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
C [auth B], D [auth A]	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
C [auth B], D [auth A]	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
C [auth B], D [auth A]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C [auth B], D [auth A]	IPR001611	Leucine-rich repeat	Repeat
C [auth B], D [auth A]	IPR017241	Toll-like receptor	Family
C [auth B], D [auth A]	IPR003591	Leucine-rich repeat, typical subtype	Repeat

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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.

8WRY | pdb_00008wry

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 Complex

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage