Warning
You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.
Contact us
Toggle navigation
RCSB PDB
Deposit
Prepare Data
PDBx/mmCIF file
pdb_extract
SF-Tool
Ligand Expo
MAXIT
Validate Data
Validation Server
Validation API
Information for Journals
Validation Task Forces
Deposit Data
wwPDB OneDep System
PDB-Dev
Help and Resources
Deposit FAQ
Validation FAQ
Tutorials
Annotation Policies
Processing Procedures
PDBx/mmCIF Dictionary
PDBx/mmCIF User Guide
Chemical Component Dictionary
Biologically Interesting Molecule Reference Dictionary (BIRD)
BioSync/Beamlines/Facilities
Related Tools
Search
Advanced Search
Sequence Similarity Search
Structure Similarity Search
Chemical Similarity Search
Chemical Sketch Tool
Browse by Annotations
New Entries
Unreleased Entries
PDB Statistics
Visualize
Mol* (MolStar)
Sequence Annotations Viewer
Genome View
Analyze
Pairwise Structure Alignment
Symmetry Resources in the PDB
Structure Quality
Grouping Structures
PDB Citation MeSH Network Explorer
PDB Statistics
EPPIC Biological Assemblies
External Data and Resources
Integrated Resources
Additional Resources
Download
Coordinates and Experimental Data
Sequences
Ligands
File Download Services
Web APIs
Learn
Training Courses
Guide to PDB Data
Molecule of the Month
Educational Resources
Curricula
Browse
News
SciArt Galleries
Irving Geis
David Goodsell
About
Contact Us
About RCSB PDB
Vision and Mission
Citation, Usage, Privacy Policies, Logo
News
PDB History
PDB50
User Community
Publications
RCSB PDB Advisory Committee
Team Members
Diversity, Equity, Inclusion, and Access
Service Status
Documentation
General Help
3D Structures in the Protein Data Bank
Computed Structure Models (CSM)
Search and Browse
Basic Search
Advanced Search
Browse Annotations
Visualize and Analyze
Sequence Viewers
Pairwise Structure Alignment
Exploring a 3D Structure
Grouping Structures
Programmatic Access
Additional Resources
Software Supporters
Deposition Resources
FAQs
Glossary
Careers
COVID-19
226,707
Structures from the PDB
1,068,577
Computed Structure Models (CSM)
Navigation Tabs
Structure Summary
Structure
Annotations
Experiment
Sequence
Genome
Versions
Display Files
FASTA Sequence
mmCIF Format
mmCIF Format (Header)
PDB Format
PDB Format (Header)
Download Files
FASTA Sequence
PDBx/mmCIF Format
PDBx/mmCIF Format (gz)
BinaryCIF Format (gz)
PDB Format
PDB Format (gz)
PDBML/XML Format (gz)
Structure Factors (CIF)
Structure Factors (CIF - gz)
Validation Full PDF
Validation (XML - gz)
Validation (CIF - gz)
Validation 2fo-fc coefficients (CIF - gz)
Validation fo-fc coefficients (CIF - gz)
Biological Assembly 1 (CIF - gz)
Biological Assembly 1 (PDB - gz)
Data API
8YTD
Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides
External Resource: Annotation
Domain Annotation: SCOP2 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)
Gene Ontology: Gene Product Annotation
Gene Ontology Database Homepage
Chains
Polymer
Molecular Function
Biological Process
Cellular Component
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
organic cyclic compound 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
Less
response to stimulus
response to chemical
response to xenobiotic stimulus
protein phosphorylation
protein autophosphorylation
phosphorylation
cellular metabolic process
primary metabolic process
peptidyl-tyrosine modification
peptidyl-tyrosine autophosphorylation
macromolecule modification
peptidyl-amino acid modification
phosphate-containing compound metabolic process
metabolic process
response to stimulus
response to chemical
response to xenobiotic stimulus
protein phosphorylation
protein autophosphorylation
phosphorylation
cellular metabolic process
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
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
detection of stimulus involved in sensory perception of pain
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
positive regulation of DNA-binding transcription factor activity
cellular biosynthetic process
positive regulation of NF-kappaB transcription factor activity
RNA metabolic process
regulation of primary metabolic process
nucleobase-containing compound metabolic process
RNA biosynthetic process
positive regulation of molecular function
nucleic acid biosynthetic process
DNA-templated transcription
regulation of RNA metabolic process
regulation of nucleobase-containing compound metabolic process
regulation of RNA biosynthetic process
regulation of biosynthetic process
regulation of cellular metabolic process
regulation of macromolecule metabolic process
nucleobase-containing compound biosynthetic process
gene expression
macromolecule biosynthetic process
nucleic acid metabolic process
regulation of cellular biosynthetic process
regulation of molecular function
regulation of gene expression
biosynthetic process
regulation of DNA-binding transcription factor activity
regulation of macromolecule biosynthetic process
regulation of DNA-templated transcription
regulation of metabolic process
programmed cell death involved in cell development
cell death
programmed cell death
response to nutrient levels
reproductive process
sex differentiation
developmental process involved in reproduction
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 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
behavior
learning or memory
cognition
neurotrophin TRK receptor signaling pathway
cell surface receptor protein tyrosine kinase signaling pathway
enzyme-linked receptor protein 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
positive regulation of phosphorylation
regulation of protein modification process
regulation of protein phosphorylation
positive regulation of protein metabolic process
positive regulation of cellular metabolic process
positive regulation of phosphate metabolic process
positive regulation of metabolic process
positive regulation of protein modification process
regulation of phosphate metabolic process
positive regulation of macromolecule metabolic process
positive regulation of protein phosphorylation
positive regulation of phosphorus metabolic process
regulation of protein metabolic process
regulation of phosphorus metabolic process
regulation of phosphorylation
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
Less
somatodendritic compartment
cell projection
dendrite
dendritic tree
neuron projection
cellular anatomical entity
plasma membrane bounded cell projection
membrane-bounded organelle
endosome membrane
intracellular anatomical structure
endosome
membrane
intracellular vesicle
late endosome membrane
somatodendritic compartment
cell projection
dendrite
dendritic tree
neuron projection
cellular anatomical entity
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
receptor complex
cell body
neuronal cell body
axon
cell surface
cell periphery
plasma membrane
early endosome
recycling endosome
recycling endosome membrane
early endosome membrane
Less
B
Macrocyclic Peptide
-
-
-
C
Macrocyclic Peptide
-
-
-
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
intellectual disability
schizophreniform disorder
sensory peripheral neuropathy
colorectal adenocarcinoma
digestive system disease
Hashimoto thyroiditis
hereditary sensory and autonomic neuropathy type 2
Less
Protein Modification Annotation
Modified Residue(s)
Chain
Residue(s)
Description
B
GM1
C
MEA
Parent Component:
PHE
RESID
: 
AA0065
PSI-MOD
:  N-methyl-L-phenylalanine
MOD:00074
About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy
Help
Contact Us
Documentation
Website FAQ
Glossary
Service Status
RCSB PDB (
citation
) is hosted by
RCSB PDB is a member of the
RCSB Partners
Nucleic Acid Knowledgebase
wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB