2NV5 | pdb_00002nv5

Crystal structure of a C-terminal phosphatase domain of Rattus norvegicus ortholog of human protein tyrosine phosphatase, receptor type, D (PTPRD)

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d2nv5c_	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d2nv5b_	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d2nv5a_	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8078131	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8078131	3000304	SCOP2B (2022-06-29)
A	SCOP2 Family	Higher-molecular-weight phosphotyrosine protein phosphatases	8078130	4000440	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Phosphotyrosine protein) phosphatases II	8078131	3000304	SCOP2 (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		e2nv5C1	A: HTH	X: HTH	H: winged helix domain	T: MarR	F:	ECOD (20:10:01)
B		e2nv5B1	A: HTH	X: HTH	H: winged helix domain	T: MarR	F:	ECOD (20:10:01)
A		e2nv5A1	A: Globin-like	X: Globin-like	H: Globin-like	T: TetR_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
B	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00102	Protein-tyrosine phosphatase (Y_phosphatase)	Protein-tyrosine phosphatase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	protein-tyrosine-phosphatase	glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding heparan sulfate proteoglycan binding glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding heparan sulfate proteoglycan binding proteoglycan binding protein tyrosine phosphatase activity heparin binding	multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation anatomical structure development regulation of biological quality system development developmental process regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis generation of neurons 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 cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis cellular component organization regulation of nervous system development neurogenesis 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 cellular component organization or biogenesis 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 plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation 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 neuron development cellular process negative regulation of collateral sprouting regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size interferon-alpha production negative regulation of type I interferon production cytokine production regulation of cytokine production regulation of interferon-alpha production negative regulation of macromolecule metabolic process regulation of biosynthetic process type I interferon production negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of interferon-alpha production metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process regulation of type I interferon production axon extension regulation of axon extension neuron projection extension negative regulation of axon extension epithelium development endothelial cell differentiation endothelium development tissue development epithelial cell differentiation endothelial cell development establishment of endothelial intestinal barrier epithelial cell development establishment of endothelial barrier head development animal organ development brain development cerebellum development central nervous system development metencephalon development hindbrain development trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of postsynaptic specialization assembly cellular component biogenesis cellular component assembly cell junction assembly regulation of excitatory synapse assembly postsynaptic density organization regulation of synapse structure or activity synapse organization regulation of synapse assembly regulation of postsynaptic density organization postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of organelle organization excitatory synapse assembly regulation of cell junction assembly regulation of synapse organization organelle organization cell junction organization regulation of organelle assembly postsynaptic specialization organization synapse assembly postsynaptic density assembly regulation of postsynaptic density assembly forebrain development pallium development cerebral cortex development telencephalon development presynapse organization presynapse assembly corpus callosum development negative regulation of dendritic spine development regulation of dendritic spine development dendrite development dendritic spine development spinal cord development hippocampus development limbic system development cellular response to stimulus positive regulation of response to biotic stimulus regulation of toll-like receptor 9 signaling pathway pattern recognition receptor signaling pathway response to stimulus regulation of signal transduction response to biotic stimulus intracellular signal transduction immune response-activating signaling pathway positive regulation of immune response negative regulation of toll-like receptor 9 signaling pathway regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response negative regulation of response to stimulus defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process cell adhesion cell-cell adhesion synaptic membrane adhesion regulation of interferon-beta production interferon-beta production negative regulation of interferon-beta production regulation of cellular response to stress negative regulation of neuron projection regeneration regeneration neuron projection regeneration response to wounding regulation of axon regeneration negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration response to axon injury regulation of response to wounding cellular response to stress axon regeneration negative regulation of response to wounding	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 intracellular anatomical structure cytoplasm cytosol presynapse presynaptic membrane glutamatergic synapse membrane-bounded organelle intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle 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 organelle membrane exocytic vesicle axon cell projection neuron projection plasma membrane bounded cell projection growth cone distal axon site of polarized growth Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C	IPR003599	Immunoglobulin domain subtype	Domain
A, B, C	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C	IPR007110	Immunoglobulin-like domain	Domain
A, B, C	IPR003598	Immunoglobulin subtype 2	Domain
A, B, C	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B, C	IPR013098	Immunoglobulin I-set	Domain
A, B, C	IPR050713	Receptor-type Tyrosine-protein Phosphatases/Ushers	Family
A, B, C	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B, C	IPR003961	Fibronectin type III	Domain
A, B, C	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B, C	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A, B, C	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

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.