4PBV | pdb_00004pbv

Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d4pbve1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
D	d4pbvd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
C	d4pbvc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	mRNA_triPase	e4pbvE1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: mRNA_triPase	ECOD (v294.1)
D	mRNA_triPase	e4pbvD1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: mRNA_triPase	ECOD (v294.1)
C	mRNA_triPase	e4pbvC1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: mRNA_triPase	ECOD (v294.1)
B	mRNA_triPase	e4pbvB1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: mRNA_triPase	ECOD (v294.1)
A	mRNA_triPase	e4pbvA1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: mRNA_triPase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	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
C, D, E	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
C, D, E	PF07679	Immunoglobulin I-set domain (I-set)	Immunoglobulin I-set domain		Domain
A, B	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A, B	PF16920	Leucine rich repeat C-terminal motif (LRRCT_2)	Leucine rich repeat C-terminal motif	-	Motif
A, B	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, E	Protein-tyrosine phosphatase CRYPalpha1 isoform	phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity phosphatase activity hydrolase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity heparin binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity phosphatase activity hydrolase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding heparan sulfate proteoglycan binding proteoglycan binding	multicellular organismal process regulation of developmental process cellular developmental process cell projection organization negative regulation of biological process cell development negative regulation of dendritic spine development regulation of dendritic spine development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation multicellular organismal process regulation of developmental process cellular developmental process cell projection organization negative regulation of biological process cell development negative regulation of dendritic spine development regulation of dendritic spine development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process dendritic spine development regulation of biological process plasma membrane bounded cell projection organization negative regulation of developmental process biological regulation nervous system development generation of neurons neuron development cellular process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth regulation of cell differentiation regulation of neurogenesis regulation of cell development cell projection morphogenesis negative regulation of growth neuron projection morphogenesis regulation of biological quality negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting regulation of cellular component organization plasma membrane bounded cell projection morphogenesis cell growth cell morphogenesis regulation of nervous system development negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth developmental cell growth growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development negative regulation of collateral sprouting regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size axon extension regulation of axon extension neuron projection extension negative regulation of axon extension cell adhesion cell junction organization cell-cell adhesion synaptic membrane adhesion synapse organization cellular response to stimulus response to stimulus signaling signal transduction cell communication regulation of cellular response to stress negative regulation of neuron projection regeneration regeneration neuron projection regeneration response to wounding regulation of axon regeneration response to external stimulus regulation of response to stimulus negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration regulation of response to external stimulus response to axon injury regulation of response to wounding cellular response to stress axon regeneration regulation of response to stress response to stress negative regulation of response to stimulus negative regulation of response to wounding protein dephosphorylation dephosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process peptidyl-tyrosine dephosphorylation	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region somatodendritic compartment cell body perikaryon neuronal cell body growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth membrane-bounded organelle intracellular anatomical structure intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane secretory vesicle cytoplasm organelle membrane exocytic vesicle
A, B	NT-3 growth factor receptor	molecular transducer activity catalytic activity, acting on a protein 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 molecular transducer activity catalytic activity, acting on a protein 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 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 neurotrophin receptor activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular developmental process cell differentiation cellular process cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular developmental process cell differentiation cellular process cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling 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 positive regulation of cellular component organization cell projection organization cell development neuron projection development cellular component organization neurogenesis neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex receptor complex axon cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, E	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D, E	IPR003598	Immunoglobulin subtype 2	Domain
C, D, E	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
C, D, E	IPR003599	Immunoglobulin domain subtype	Domain
C, D, E	IPR013098	Immunoglobulin I-set	Domain
C, D, E	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
C, D, E	IPR050713	Receptor-type Tyrosine-protein Phosphatases/Ushers	Family
C, D, E	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
C, D, E	IPR003961	Fibronectin type III	Domain
C, D, E	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
C, D, E	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
C, D, E	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D, E	IPR007110	Immunoglobulin-like domain	Domain
C, D, E	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR013098	Immunoglobulin I-set	Domain
A, B	IPR002011	Tyrosine-protein kinase, receptor class II, conserved site	Conserved Site
A, B	IPR001611	Leucine-rich repeat	Repeat
A, B	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
A, B	IPR020446	NT-3 growth factor receptor NTRK3	Family
A, B	IPR020777	Growth factor receptor NTRK	Family
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR031635	Growth factor receptor NTRK, leucine rich repeat C-terminal	Domain
A, B	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR050122	Receptor Tyrosine Kinase	Family
A, B	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
A, B	IPR007110	Immunoglobulin-like domain	Domain