6KIP | pdb_00006kip

Crystal structure of PTPRD phosphatase domain in complex with Liprin-alpha3 tandem SAM domains

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)
A	d6kipa1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6kipa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	SAM_1	e6kipB3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: SAM_1	ECOD (1.6)
A	Y_phosphatase	e6kipA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Y_phosphatase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.150.50	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00536	SAM domain (Sterile alpha motif) (SAM_1)	SAM domain (Sterile alpha motif)	It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module ...	It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.	Domain
B	PF07647	SAM domain (Sterile alpha motif) (SAM_2)	SAM domain (Sterile alpha motif)		Domain
A	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
B	Liprin-alpha-3	-	cellular localization regulated exocytosis transport signaling synaptic vesicle cycle synaptic vesicle exocytosis membrane docking vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization organelle localization by membrane tethering synaptic signaling secretion by cell organelle localization cellular localization regulated exocytosis transport signaling synaptic vesicle cycle synaptic vesicle exocytosis membrane docking vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization organelle localization by membrane tethering synaptic signaling secretion by cell organelle localization signal release establishment of localization in cell vesicle docking involved in exocytosis trans-synaptic signaling regulation of biological process neurotransmitter secretion secretion biological regulation export from cell cell-cell signaling neurotransmitter transport synaptic vesicle docking establishment of localization chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling vesicle docking exocytic process cellular process regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of short-term neuronal synaptic plasticity regulation of signaling regulation of cellular process modulation of chemical synaptic transmission regulation of trans-synaptic signaling regulation of cell communication regulation of biological quality	presynapse cellular anatomical structure synapse cell junction presynaptic active zone epididymosome membrane-bounded organelle extracellular vesicle extracellular organelle microvesicle extracellular region organelle vesicle extracellular membrane-bounded organelle presynapse cellular anatomical structure synapse cell junction presynaptic active zone epididymosome membrane-bounded organelle extracellular vesicle extracellular organelle microvesicle extracellular region organelle vesicle extracellular membrane-bounded organelle cell cortex intracellular anatomical structure cytoplasmic region presynaptic active zone cytoplasmic component cell periphery cell cortex region cytoplasm glutamatergic synapse acrosomal vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle secretory granule secretory vesicle
A	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 trans-synaptic signaling synaptic signaling trans-synaptic signaling by trans-synaptic complex signaling cell-cell signaling cell communication cellular response to stimulus 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 signal transduction 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	IPR037620	Liprin-alpha, SAM domain 1	Domain
B	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
B	IPR029515	Liprin	Family
B	IPR037622	Liprin-alpha, SAM domain 3	Domain
B	IPR001660	Sterile alpha motif domain	Domain
B	IPR037621	Liprin-alpha, SAM domain 2	Domain
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