8YTD | pdb_00008ytd

Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055582	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	HGTP_anticodon	e8ytdA01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: HGTP_anticodon	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Macrocyclic Peptide	-	-	-
B	Macrocyclic Peptide	-	-	-
A	High affinity nerve growth factor receptor	molecular transducer activity catalytic activity, acting on a protein GPI-linked ephrin receptor activity ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase 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 molecular transducer activity catalytic activity, acting on a protein GPI-linked ephrin receptor activity ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase 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 neurotrophin binding protein binding binding nerve growth factor binding growth factor binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding signaling receptor binding cytokine receptor binding neurotrophin receptor binding neurotrophin p75 receptor binding neurotrophin receptor activity nerve growth factor receptor activity identical protein binding kinase binding enzyme binding protein homodimerization activity protein dimerization activity	response to stimulus response to chemical response to xenobiotic stimulus protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process peptidyl-tyrosine modification peptidyl-tyrosine autophosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process metabolic process cellular process response to stimulus response to chemical response to xenobiotic stimulus protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process peptidyl-tyrosine modification peptidyl-tyrosine autophosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation protein modification process phosphorus metabolic process response to stress response to wounding response to axon injury developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation multicellular organism development multicellular organismal process anatomical structure development sympathetic nervous system development autonomic nervous system development nervous system development system development cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor regulation of neuron projection development regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development cellular component organization neurogenesis neuron differentiation positive regulation of neuron projection development cell differentiation positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation generation of neurons neuron development regulation of plasma membrane bounded cell projection organization response to electrical stimulus response to abiotic stimulus detection of external stimulus system process nervous system process response to external stimulus 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 detection of stimulus involved in sensory perception detection of temperature stimulus involved in sensory perception of pain programmed cell death involved in cell development cell death programmed cell death response to nutrient levels sex differentiation epithelial cell differentiation Sertoli cell differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development epithelium development gonad development reproductive system development Sertoli cell development animal organ development tissue development epithelial cell development cellular response to stimulus cell surface receptor signaling pathway signaling cell communication nerve growth factor signaling pathway neurotrophin signaling pathway signal transduction rhythmic process circadian rhythm hemopoiesis B cell activation cell activation mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation immune system process leukocyte differentiation positive regulation of nervous system development regulation of developmental process regulation of nervous system development positive regulation of developmental process cellular component biogenesis cellular component assembly cell junction assembly regulation of multicellular organismal process regulation of synapse structure or activity synapse organization regulation of synapse assembly regulation of biological quality regulation of multicellular organismal development 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 positive regulation of multicellular organismal process synapse assembly positive regulation of synapse assembly 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 positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic synaptic signaling trans-synaptic signaling positive regulation of synaptic transmission cell-cell signaling positive regulation of synaptic transmission, glutamatergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity mechanoreceptor differentiation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process olfactory nerve development nerve development cranial nerve development cellular response to chemical stimulus cellular response to nicotine response to nicotine axonogenesis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis axon guidance axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection guidance negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway behavior learning or memory cognition neurotrophin TRK receptor signaling pathway positive regulation of programmed cell death multicellular organismal response to stress response to pain behavioral response to formalin induced pain chemosensory behavior behavioral response to chemical pain behavioral response to pain response to acid chemical response to hydrostatic pressure response to oxygen-containing compound response to water innervation axonogenesis involved in innervation small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of Ras protein signal transduction positive regulation of Ras protein signal transduction Ras protein signal transduction positive regulation of small GTPase mediated signal transduction	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle endosome membrane intracellular anatomical structure endosome membrane intracellular vesicle late endosome membrane somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle endosome membrane intracellular anatomical structure endosome membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane protein-containing complex signaling receptor complex cell body neuronal cell body axon mitochondrion cell surface cell periphery plasma membrane early endosome recycling endosome recycling endosome membrane early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR001611	Leucine-rich repeat	Repeat
A	IPR020777	Growth factor receptor NTRK	Family
A	IPR031635	Growth factor receptor NTRK, leucine rich repeat C-terminal	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR040665	Tyrosine kinase receptor A, transmembrane domain	Domain
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR002011	Tyrosine-protein kinase, receptor class II, conserved site	Conserved Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR050122	Receptor Tyrosine Kinase	Family
A	IPR020461	High affinity nerve growth factor receptor NTRK1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04629	hereditary sensory and autonomic neuropathy type 4 familial medullary thyroid carcinoma malignant glioma neuroblastoma schizoaffective disorder Lewy body dementia neuralgia hereditary sensory and autonomic neuropathy schizophrenia Lung Injury mixed glioma bipolar disorder cancer medulloblastoma Charcot-Marie-Tooth disease hereditary sensory and autonomic neuropathy type 4 familial medullary thyroid carcinoma malignant glioma neuroblastoma schizoaffective disorder Lewy body dementia neuralgia hereditary sensory and autonomic neuropathy schizophrenia Lung Injury mixed glioma bipolar disorder cancer medulloblastoma Charcot-Marie-Tooth disease ovarian serous adenocarcinoma psoriasis hypothyroidism thyroid gland papillary carcinoma glioma non-small cell lung carcinoma hereditary sensory and autonomic neuropathy type 1 hereditary sensory and autonomic neuropathy type 5 Riley-Day syndrome schizophreniform disorder intellectual disability sensory peripheral neuropathy colorectal adenocarcinoma digestive system disease Hashimoto thyroiditis hereditary sensory and autonomic neuropathy type 2

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	MEA	Parent Component: PHE RESID: AA0065 PSI-MOD : N-methyl-L-phenylalanine MOD:00074
B	GM1	RESID: AA0065

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.

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