7CEG | pdb_00007ceg

Crystal structure of the complex between mouse PTP delta and neuroligin-3

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Acetylcholinesterase-like	8102700	4000699	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	alpha/beta-Hydrolases	8102701	3000102	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)
B	CBS	e7cegB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: CBS	ECOD (v294.1)
A	CBS	e7cegA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: CBS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00135	Carboxylesterase family (COesterase)	Carboxylesterase family		Domain
A	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
A	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain
A	PF07679	Immunoglobulin I-set domain (I-set)	Immunoglobulin I-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Neuroligin-3	cell adhesion molecule binding protein binding binding cell adhesion mediator activity signaling receptor binding neurexin family protein binding molecular transducer activity signaling receptor activity scaffold protein binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling rhythmic synaptic transmission behavior learning learning or memory cognition regulation of localization transport regulation of signaling receptor activity monoatomic ion transmembrane transport regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport localization positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport regulation of transport regulation of monoatomic ion transport establishment of localization transmembrane transport regulation of molecular function positive regulation of AMPA receptor activity regulation of transmembrane transport positive regulation of transport positive regulation of transporter activity regulation of neurotransmitter receptor activity positive regulation of ion transmembrane transporter activity positive regulation of inhibitory postsynaptic potential positive regulation of nervous system process modulation of inhibitory postsynaptic potential inhibitory postsynaptic potential positive regulation of multicellular organismal process long-term synaptic potentiation regulation of synaptic plasticity positive regulation of synaptic transmission regulation of long-term synaptic potentiation regulation of developmental process cellular developmental process cell projection organization positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development cellular component organization positive regulation of developmental process 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 plasma membrane bounded cell projection organization nervous system development generation of neurons neuron development startle response regulation of response to external stimulus neuromuscular process negative regulation of response to stimulus negative regulation of biological process prepulse inhibition response to external stimulus negative regulation of response to external stimulus cell adhesion cell-cell adhesion neuron cell-cell adhesion axon extension axonogenesis developmental growth plasma membrane bounded cell projection morphogenesis cell growth cell morphogenesis cell projection morphogenesis neuron projection morphogenesis neuron projection extension developmental cell growth growth axon development cell morphogenesis involved in neuron differentiation developmental growth involved in morphogenesis anatomical structure morphogenesis cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly import into cell receptor-mediated endocytosis endocytosis vesicle-mediated transport regulation of cellular component organization presynapse organization regulation of terminal button organization terminal button organization regulation of synapse organization regulation of presynapse organization regulation of synapse structure or activity protein localization to synapse regulation of protein localization positive regulation of protein localization to synapse regulation of protein localization to synapse macromolecule localization positive regulation of protein localization intracellular protein localization protein localization to cell junction synaptic vesicle endocytosis cellular localization synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell positive regulation of nervous system development positive regulation of cellular component organization regulation of nervous system development regulation of synapse assembly 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 positive regulation of synapse assembly central nervous system development gliogenesis oligodendrocyte differentiation glial cell differentiation postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly organelle organization postsynaptic specialization organization dendritic spine morphogenesis dendritic spine organization regulation of cell projection organization regulation of postsynapse organization regulation of neuron projection development regulation of anatomical structure morphogenesis dendrite morphogenesis regulation of dendritic spine morphogenesis neuron projection organization regulation of plasma membrane bounded cell projection organization synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic membrane organization membrane biogenesis presynaptic membrane assembly membrane assembly presynaptic membrane organization presynapse assembly regulation of NMDA receptor activity adult behavior respiratory gaseous exchange by respiratory system respiratory system process regulation of respiratory gaseous exchange regulation of respiratory system process regulation of respiratory gaseous exchange by nervous system process vesicle localization synaptic vesicle clustering organelle localization positive regulation of synaptic vesicle clustering regulation of synaptic vesicle clustering synaptic vesicle localization response to light stimulus visual learning visual behavior associative learning response to radiation response to abiotic stimulus rhythmic process circadian sleep/wake cycle circadian behavior rhythmic behavior circadian rhythm glutamate receptor signaling pathway positive regulation of glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway negative regulation of dendritic spine morphogenesis negative regulation of cellular component organization negative regulation of dendritic spine development negative regulation of cellular process negative regulation of cell projection organization negative regulation of developmental process negative regulation of neuron projection development biological process involved in intraspecies interaction between organisms social behavior negative regulation of excitatory postsynaptic potential postsynaptic membrane assembly postsynaptic membrane organization vocalization behavior	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane somatodendritic compartment cell projection dendrite dendritic tree cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle endocytic vesicle glutamatergic synapse cell body neuronal cell body inhibitory synapse cell surface postsynaptic specialization membrane postsynaptic specialization presynapse GABA-ergic synapse excitatory synapse
A	Isoform C of Receptor-type tyrosine-protein phosphatase delta	protein binding binding signaling receptor binding cell adhesion molecule 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	positive regulation of nervous system development multicellular organismal process regulation of cellular process positive regulation of cellular component organization regulation of cellular component organization regulation of developmental process positive regulation of biological process regulation of nervous system development positive regulation of developmental process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development positive regulation of nervous system development multicellular organismal process regulation of cellular process positive regulation of cellular component organization regulation of cellular component organization regulation of developmental process positive regulation of biological process regulation of nervous system development positive regulation of developmental process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development regulation of multicellular organismal process regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality positive regulation of cellular process system development developmental process regulation of multicellular organismal development regulation of biological process positive regulation of cellular component biogenesis biological regulation nervous system development 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 cellular process synapse assembly positive regulation of synapse assembly membrane organization presynapse organization membrane biogenesis presynaptic membrane assembly membrane assembly presynaptic membrane organization presynapse assembly cell adhesion cell-cell adhesion synaptic membrane adhesion response to stimulus regulation of response to stimulus immune response immune system process regulation of immune response regulation of immune system process heterophilic cell-cell adhesion cellular developmental process generation of neurons neurogenesis neuron differentiation cell differentiation cellular response to stimulus signaling signal transduction cell communication trans-synaptic signaling synaptic signaling trans-synaptic signaling by trans-synaptic complex cell-cell signaling cell surface receptor signaling pathway via STAT negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of cellular process regulation of receptor signaling pathway via JAK-STAT negative regulation of receptor signaling pathway via JAK-STAT regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of cell communication negative regulation of receptor signaling pathway via STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT modulation of chemical synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of postsynaptic specialization assembly regulation of excitatory synapse assembly postsynaptic density organization regulation of postsynaptic density organization postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly regulation of postsynapse organization regulation of organelle organization excitatory synapse assembly organelle organization regulation of organelle assembly postsynaptic specialization organization postsynaptic density assembly regulation of postsynaptic density assembly cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell morphogenesis regulation of cell development cell projection morphogenesis neuron projection morphogenesis regulation of dendrite morphogenesis positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development regulation of neuron projection development plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis positive regulation of cell differentiation dendrite development positive regulation of neurogenesis regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization positive regulation of dendrite morphogenesis dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization positive regulation of dendritic spine morphogenesis positive regulation of dendritic spine development dendritic spine morphogenesis dendritic spine development dendritic spine organization regulation of dendritic spine development positive regulation of neuron projection development regulation of dendritic spine morphogenesis neuron projection organization	cell periphery presynapse cellular anatomical structure synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane glutamatergic synapse neuron to neuron synapse hippocampal mossy fiber to CA3 synapse Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR051093	Neuroligin and Bile salt-activated lipase	Family
B	IPR002018	Carboxylesterase, type B	Domain
B	IPR019819	Carboxylesterase type B, conserved site	Conserved Site
B	IPR000460	Neuroligin	Family
B	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR003598	Immunoglobulin subtype 2	Domain
A	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR013098	Immunoglobulin I-set	Domain
A	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A	IPR050713	Receptor-type Tyrosine-protein Phosphatases/Ushers	Family
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR003961	Fibronectin type III	Domain
A	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR045905	Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1	Domain
A	IPR036116	Fibronectin type III superfamily	Homologous Superfamily