4ZBN

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor

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)
C [auth A]	SCOP2B Superfamily	Cystine-knot cytokines	8038796	3000846	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Cystine-knot cytokines	8038796	3000846	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)
C [auth A]	NGF	e4zbnA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: NGF	ECOD (1.6)
D [auth B]	NGF	e4zbnB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: NGF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF00243	Nerve growth factor family (NGF)	Nerve growth factor family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth E]	DNA (28-MER)	-	-	-
C [auth A], D [auth B]	Beta-nerve growth factor	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 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 enzyme regulator activity molecular function inhibitor activity peptidase regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity metalloendopeptidase inhibitor activity endopeptidase inhibitor activity lipid binding	regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA 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 regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA 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 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 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 cellular metabolic process 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 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 behavior multicellular organismal 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 cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway 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 positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of neuron differentiation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation peripheral nervous system development positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth regulation of neurogenesis regulation of cell development positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth positive regulation of collateral sprouting regulation of cell projection organization positive regulation of cell development developmental growth involved in morphogenesis positive regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting regulation of cellular component organization positive regulation of cellular component organization cell growth regulation of nervous system development regulation of extent of cell growth regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis positive regulation of axonogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size nerve development positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette positive regulation of Ras protein signal transduction Ras protein signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus positive regulation of small GTPase mediated signal transduction positive regulation of signaling cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle extracellular region axon extracellular space endosome intracellular vesicle cytoplasmic vesicle endosome lumen vesicle transport vesicle synapse presynapse synaptic vesicle cell junction secretory vesicle exocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR020408	Nerve growth factor-like	Family
C [auth A], D [auth B]	IPR019846	Nerve growth factor conserved site	Conserved Site
C [auth A], D [auth B]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
C [auth A], D [auth B]	IPR020437	Nerve growth factor, beta subunit, mammalian	Family
C [auth A], D [auth B]	IPR002072	Nerve growth factor-related	Domain
C [auth A], D [auth B]	IPR020425	Nerve growth factor, beta subunit	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], D [auth B]	Pharos: P01138	hereditary sensory and autonomic neuropathy type 5 peripheral neuropathy neurodegenerative disease glomerulonephritis status epilepticus Nerve Degeneration corneal ulcer cystitis epilepsy with generalized tonic-clonic seizures interstitial nephritis peripheral nervous system disease Lewy body dementia middle cerebral artery infarction cocaine abuse nervous system disorder hereditary sensory and autonomic neuropathy type 5 peripheral neuropathy neurodegenerative disease glomerulonephritis status epilepticus Nerve Degeneration corneal ulcer cystitis epilepsy with generalized tonic-clonic seizures interstitial nephritis peripheral nervous system disease Lewy body dementia middle cerebral artery infarction cocaine abuse nervous system disorder overactive bladder Parkinson disease dissociative amnesia chronic kidney disease hereditary sensory and autonomic neuropathy hereditary sensory and autonomic neuropathy type 4 cocaine dependence heroin dependence visual epilepsy malignant mesothelioma hereditary sensory and autonomic neuropathy type 1 chronic renal failure syndrome sensory peripheral neuropathy toxic encephalopathy depressive disorder autosomal recessive juvenile Parkinson disease 2 phaeochromocytoma Charcot-Marie-Tooth disease Riley-Day syndrome heart disease hereditary sensory and autonomic neuropathy type 2 hydrolethalus syndrome alcohol withdrawal amnestic disorder cancer cystic fibrosis parkinsonian disorder intellectual disability cerebrovascular disorder

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.