1HCF

Crystal structure of TrkB-d5 bound to neurotrophin-4/5

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1hcfa_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Neurotrophin	Neurotrophin 4, NT4	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1hcfb_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Neurotrophin	Neurotrophin 4, NT4	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth X]	d1hcfx_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Ligand binding domain of trkB receptor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth Y]	d1hcfy_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Ligand binding domain of trkB receptor	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	Neurotrophin	8024040	4003445	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cystine-knot cytokines	8036419	3000846	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cystine-knot cytokines	8036419	3000846	SCOP2B (2022-06-29)
C [auth X]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054813	3000071	SCOP2B (2022-06-29)
D [auth Y]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054813	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	PF00243	e1hcfA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00243	ECOD (1.6)
B	PF00243	e1hcfB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00243	ECOD (1.6)
C [auth X]	PF07679	e1hcfX1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07679	ECOD (1.6)
D [auth Y]	PF07679	e1hcfY1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07679	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
C [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00243	Nerve growth factor family (NGF)	Nerve growth factor family	-	Domain
C [auth X], D [auth Y]	PF07679	Immunoglobulin I-set domain (I-set)	Immunoglobulin I-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NEUROTROPHIN-4	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity nerve growth factor receptor binding cytokine receptor binding neurotrophin receptor binding tumor necrosis factor receptor superfamily binding death receptor binding	cellular response to stimulus regulation of biological process cellular response to growth factor stimulus regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cellular response to nerve growth factor stimulus cell communication cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway cellular response to stimulus regulation of biological process cellular response to growth factor stimulus regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cellular response to nerve growth factor stimulus cell communication cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway response to nerve growth factor cellular process response to growth factor signal transduction developmental process multicellular organismal process sensory organ development animal organ development sensory organ boundary specification pattern specification process formation of anatomical boundary regionalization anatomical structure morphogenesis multicellular organism development anatomical structure formation involved in morphogenesis anatomical structure development formation of animal organ boundary animal organ formation animal organ morphogenesis adult locomotory behavior behavior adult behavior locomotory behavior mechanoreceptor differentiation cellular developmental process nervous system development generation of neurons neurogenesis neuron differentiation cell differentiation system development epidermis development tissue development positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of peptidyl-serine phosphorylation positive regulation of cellular metabolic process positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process positive regulation of cellular process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process system process learning or memory nervous system process cognition memory neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization neuron development cell fate determination ganglion mother cell fate determination cell fate commitment long-term memory trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of developmental process regulation of cell differentiation regulation of neuron differentiation peripheral nervous system development tongue development taste bud development nerve development innervation cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway	somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection extracellular region axon extracellular space membrane-bounded organelle intracellular anatomical structure transport vesicle synapse somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection extracellular region axon extracellular space membrane-bounded organelle intracellular anatomical structure transport vesicle synapse intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle organelle cell junction secretory vesicle cytoplasm vesicle exocytic vesicle
C [auth X], D [auth Y]	BDNF/NT-3 GROWTH FACTORS RECEPTOR	neurotrophin binding brain-derived neurotrophic factor binding protein binding binding growth factor binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding neurotrophin binding brain-derived neurotrophic factor binding protein binding binding growth factor binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding brain-derived neurotrophic factor receptor activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity neurotrophin receptor activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity enzyme binding protease binding identical protein binding protein homodimerization activity protein dimerization activity	developmental process multicellular organismal process cellular developmental process central nervous system neuron development cell development nervous system development generation of neurons central nervous system neuron differentiation multicellular organism development neurogenesis central nervous system development neuron differentiation cell differentiation neuron development anatomical structure development developmental process multicellular organismal process cellular developmental process central nervous system neuron development cell development nervous system development generation of neurons central nervous system neuron differentiation multicellular organism development neurogenesis central nervous system development neuron differentiation cell differentiation neuron development anatomical structure development cellular process system development behavior system process learning learning or memory nervous system process cognition cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor peripheral nervous system axon ensheathment peripheral nervous system development glial cell development myelination Schwann cell development gliogenesis axon ensheathment ensheathment of neurons glial cell differentiation myelination in peripheral nervous system Schwann cell differentiation regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of programmed cell death regulation of apoptotic process regulation of anoikis negative regulation of biological process regulation of programmed cell death cell death negative regulation of anoikis negative regulation of apoptotic process anoikis negative regulation of cellular process apoptotic process programmed cell death positive regulation of nervous system development axonogenesis cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron projection morphogenesis positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis cell morphogenesis cellular component organization regulation of nervous system development positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis regulation of plasma membrane bounded cell projection organization positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation trans-synaptic signaling regulation of signaling signaling trans-synaptic signaling, modulating synaptic transmission modulation of chemical synaptic transmission cell-cell signaling cell communication chemical synaptic transmission trans-synaptic signaling by BDNF, modulating synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication trans-synaptic signaling by BDNF trans-synaptic signaling by neuropeptide, modulating synaptic transmission synaptic signaling via neuropeptide trans-synaptic signaling by neuropeptide protein autophosphorylation positive regulation of neuron projection development head development forebrain development animal organ development brain development pallium development cerebral cortex development telencephalon development cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical response to organic substance cellular response to chemical stimulus response to chemical response to amino acid amyloid precursor protein catabolic process regulation of amide metabolic process regulation of amyloid-beta formation regulation of amyloid precursor protein catabolic process negative regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process amide metabolic process amyloid precursor protein metabolic process negative regulation of protein metabolic process amyloid-beta formation negative regulation of macromolecule metabolic process negative regulation of amyloid-beta formation negative regulation of amide metabolic process negative regulation of metabolic process regulation of molecular function regulation of catalytic activity regulation of hydrolase activity regulation of GTPase activity action potential propagation action potential transmission of nerve impulse neuronal action potential propagation regulation of biological quality regulation of membrane potential cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway brain-derived neurotrophic factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway rhythmic process circadian rhythm cellular component biogenesis cellular component assembly cell junction assembly regulation of synapse structure or activity synapse organization regulation of synapse assembly positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly positive regulation of synapse assembly oligodendrocyte differentiation organic anion transport nitrogen compound transport carboxylic acid transport transport secretion organic substance transport export from cell establishment of localization organic acid transport amino acid transport localization acidic amino acid transport secretion by cell dicarboxylic acid transport glutamate secretion mechanoreceptor differentiation positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process feeding behavior cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation sensory organ development photoreceptor cell differentiation visual system development retina development in camera-type eye neural retina development eye morphogenesis retinal rod cell development eye photoreceptor cell differentiation animal organ morphogenesis sensory system development photoreceptor cell development camera-type eye morphogenesis eye development eye photoreceptor cell development camera-type eye photoreceptor cell differentiation retina morphogenesis in camera-type eye sensory organ morphogenesis camera-type eye development retinal rod cell differentiation positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade peripheral nervous system neuron development peripheral nervous system neuron differentiation blood vessel morphogenesis tube development vasculogenesis vasculature development circulatory system development tube morphogenesis blood vessel development neuron migration cell migration cell motility long-term synaptic potentiation regulation of synaptic plasticity positive regulation of synaptic transmission	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection protein-containing complex receptor complex neuron spine synapse intracellular anatomical structure cytoplasm cellular anatomical entity cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection protein-containing complex receptor complex neuron spine synapse dendritic spine postsynapse cell junction perinuclear region of cytoplasm axon axon terminus presynapse distal axon terminal bouton neuron projection terminus cell periphery plasma membrane membrane membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle endosome membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR020408	Nerve growth factor-like	Family
A, B	IPR019846	Nerve growth factor conserved site	Conserved Site
A, B	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B	IPR002072	Nerve growth factor-related	Domain
A, B	IPR020432	Neurotrophin-4	Family
C [auth X], D [auth Y]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth X], D [auth Y]	IPR008266	Tyrosine-protein kinase, active site	Active Site
C [auth X], D [auth Y]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
C [auth X], D [auth Y]	IPR000719	Protein kinase domain	Domain
C [auth X], D [auth Y]	IPR001611	Leucine-rich repeat	Repeat
C [auth X], D [auth Y]	IPR020777	Growth factor receptor NTRK	Family
C [auth X], D [auth Y]	IPR031635	Growth factor receptor NTRK, leucine rich repeat C-terminal	Domain
C [auth X], D [auth Y]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth X], D [auth Y]	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
C [auth X], D [auth Y]	IPR007110	Immunoglobulin-like domain	Domain
C [auth X], D [auth Y]	IPR017441	Protein kinase, ATP binding site	Binding Site
C [auth X], D [auth Y]	IPR000372	Leucine-rich repeat N-terminal domain	Domain
C [auth X], D [auth Y]	IPR003599	Immunoglobulin subtype	Domain
C [auth X], D [auth Y]	IPR003598	Immunoglobulin subtype 2	Domain
C [auth X], D [auth Y]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
C [auth X], D [auth Y]	IPR013098	Immunoglobulin I-set	Domain
C [auth X], D [auth Y]	IPR002011	Tyrosine-protein kinase, receptor class II, conserved site	Conserved Site
C [auth X], D [auth Y]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C [auth X], D [auth Y]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C [auth X], D [auth Y]	IPR020455	BDNF/NT-3 growth factors receptor NTRK2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P34130	glaucoma 1, open angle, O intellectual disability Nerve Degeneration autism glaucoma bipolar disorder
C [auth X], D [auth Y]	Pharos: Q16620	obesity disorder pilocytic astrocytoma malignant glioma obesity, hyperphagia, and developmental delay status epilepticus astrocytic tumor neuroblastoma childhood cerebral astrocytoma fibrillary astrocytoma Hyperphagia juvenile pilocytic astrocytoma cocaine abuse Lewy body dementia anaplastic astrocytoma gemistocytic astrocytoma obesity disorder pilocytic astrocytoma malignant glioma obesity, hyperphagia, and developmental delay status epilepticus astrocytic tumor neuroblastoma childhood cerebral astrocytoma fibrillary astrocytoma Hyperphagia juvenile pilocytic astrocytoma cocaine abuse Lewy body dementia anaplastic astrocytoma gemistocytic astrocytoma non-small cell lung carcinoma cocaine dependence protoplasmic astrocytoma subependymal giant cell astrocytoma mixed glioma bipolar disorder Pick disease large cell medulloblastoma lung cancer psoriasis depressive disorder malignant ependymoma schizophrenia developmental disability malignant pancreatic neoplasm Duchenne muscular dystrophy medulloblastoma acquired metabolic disease ulcerative colitis Emery-Dreifuss muscular dystrophy asthma nasopharyngeal carcinoma atopic eczema glioma autism breast cancer pancreatic intraductal papillary-mucinous carcinoma paranoid schizophrenia primitive neuroectodermal tumor lung carcinoma developmental and epileptic encephalopathy, 58 diffuse astrocytoma ductal breast carcinoma in situ alcohol-related birth defect epilepsy mood disorder atrial fibrillation breast carcinoma pancreatic intraductal papillary-mucinous neoplasm Kleine-Levin syndrome pituitary cancer lung adenocarcinoma major depressive disorder rhinitis Down syndrome dysthymic disorder anxiety disorder West syndrome esophageal adenocarcinoma astrocytoma (excluding glioblastoma) glioblastoma neurodegenerative disease atypical teratoid rhabdoid tumor oligodendroglioma cerebral astrocytoma invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia