6L03 | pdb_00006l03

structure of PTP-MEG2 and MUNC18-1-pY145 peptide complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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	(Phosphotyrosine protein) phosphatases II	8078041	3000304	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Y_phosphatase	e6l03A1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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 [auth F]	stxbp1-pY145 peptide	protein binding binding SNARE binding syntaxin binding identical protein binding phospholipase binding enzyme binding protein domain specific binding syntaxin-1 binding RNA binding nucleic acid binding kinase binding protein kinase binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization membrane organization protein-containing complex organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization regulation of protein stability biological regulation regulation of biological quality protein stabilization membrane organization protein-containing complex organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization organelle fusion localization organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular process cellular component organization or biogenesis vesicle fusion establishment of organelle localization multicellular organismal process regulation of immune effector process regulation of localization regulated exocytosis regulation of myeloid leukocyte mediated immunity regulation of cellular process response to stimulus cell activation involved in immune response leukocyte degranulation myeloid leukocyte activation myeloid leukocyte mediated immunity positive regulation of leukocyte degranulation positive regulation of regulated secretory pathway establishment of localization in cell leukocyte mediated immunity regulation of immune system process positive regulation of mast cell degranulation positive regulation of immune system process regulation of biological process immune response vacuolar localization mast cell degranulation immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis lysosome localization cellular localization positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis regulation of mast cell degranulation leukocyte activation regulation of regulated secretory pathway secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization leukocyte activation involved in immune response mast cell activation positive regulation of immune effector process regulation of leukocyte degranulation positive regulation of cellular process mast cell mediated immunity secretion regulation of transport cell activation export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response mast cell activation involved in immune response positive regulation of transport immune system process regulation of exocytosis regulation of body fluid levels wound healing homotypic cell-cell adhesion hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion response to stress coagulation response to wounding platelet activation protein localization to cell periphery protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane regulation of cellular component organization negative regulation of cellular component organization negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly negative regulation of cellular process trans-synaptic signaling signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling anterograde trans-synaptic signaling neuromuscular synaptic transmission synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse regulation of synaptic vesicle membrane organization endomembrane system organization vesicle fusion to plasma membrane neurotransmitter secretion neurotransmitter transport regulation of organelle organization signal release from synapse regulation of vesicle fusion signal release regulation of synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle membrane organization exocytic process regulation of calcium ion-dependent exocytosis calcium-ion regulated exocytosis positive regulation of calcium ion-dependent exocytosis synaptic vesicle priming regulation of synaptic vesicle priming dense core granule localization presynaptic dense core vesicle exocytosis secretory granule localization vesicle localization calcium ion-regulated exocytosis of neurotransmitter establishment of vesicle localization neuronal dense core vesicle exocytosis dense core granule exocytosis negative regulation of synaptic transmission, GABAergic negative regulation of signaling modulation of chemical synaptic transmission negative regulation of synaptic transmission negative regulation of cell communication regulation of signaling synaptic transmission, GABAergic regulation of trans-synaptic signaling regulation of cell communication regulation of synaptic transmission, GABAergic sexual reproduction reproductive process fertilization acrosome reaction single fertilization acrosomal vesicle exocytosis regulation of acrosomal vesicle exocytosis membrane docking organelle localization by membrane tethering positive regulation of vesicle docking vesicle docking regulation of vesicle docking vesicle docking involved in exocytosis regulation of SNARE complex assembly neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process establishment of protein localization nitrogen compound transport intracellular transport protein transport intracellular protein transport biological process involved in interspecies interaction between organisms response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus response to peptide response to chemical defense response to other organism innate immune response cellular response to cytokine stimulus response to external biotic stimulus axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization axon target recognition nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development platelet degranulation regulation of synaptic plasticity long-term synaptic depression developmental process involved in reproduction synaptic vesicle maturation developmental maturation positive regulation of cell communication synaptic transmission, glutamatergic regulation of glutamate secretion positive regulation of neurotransmitter secretion positive regulation of amine transport regulation of amino acid transport glutamate secretion positive regulation of neurotransmitter transport carboxylic acid transport positive regulation of synaptic transmission organic acid transport acidic amino acid transport glutamate secretion, neurotransmission positive regulation of glutamate secretion, neurotransmission positive regulation of amino acid transport dicarboxylic acid transport regulation of synaptic transmission, glutamatergic L-amino acid transport L-glutamate import organic anion transport regulation of neurotransmitter transport positive regulation of glutamate secretion positive regulation of synaptic transmission, glutamatergic positive regulation of organic acid transport amino acid transport amine transport regulation of glutamate secretion, neurotransmission regulation of neurotransmitter secretion regulation of organic acid transport regulation of amine transport positive regulation of signaling response to lipid response to estradiol response to oxygen-containing compound	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol parallel fiber to Purkinje cell synapse extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol parallel fiber to Purkinje cell synapse synapse cell junction excitatory synapse intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle secretory granule secretory vesicle cell cortex cytoplasmic region presynaptic active zone cytoplasmic component cell periphery presynapse cell cortex region presynaptic active zone glutamatergic synapse perinuclear region of cytoplasm axon cell projection neuron projection plasma membrane bounded cell projection postsynapse mitochondrion cytosolic region presynaptic cytosol phagocytic vesicle endocytic vesicle plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex platelet alpha granule extrinsic component of plasma membrane presynaptic membrane synaptic membrane extrinsic component of synaptic membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane
A	Tyrosine-protein phosphatase non-receptor type 9	phosphoric ester hydrolase activity phosphoprotein phosphatase activity non-membrane spanning protein tyrosine 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 protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery regulation of biological process protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of protein localization to plasma membrane 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 regulation of neuron projection development multicellular organismal process regulation of cellular component organization cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization cellular response to stimulus response to stimulus signaling signal transduction cell communication	cell projection cellular anatomical structure neuron projection terminus neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cell projection cellular anatomical structure neuron projection terminus neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth F]	IPR043154	Sec1-like, domain 1	Homologous Superfamily
B [auth F]	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
B [auth F]	IPR001619	Sec1-like protein	Family
B [auth F]	IPR036045	Sec1-like superfamily	Homologous Superfamily
B [auth F]	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A	IPR001251	CRAL-TRIO lipid binding domain	Domain
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A	IPR036865	CRAL-TRIO lipid binding domain superfamily	Homologous Superfamily
A	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A	IPR011074	CRAL/TRIO, N-terminal domain	Domain
A	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A	IPR050348	Protein-Tyrosine Phosphatase	Family
A	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A	IPR036273	CRAL/TRIO, N-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth F]	Pharos: P61764	developmental and epileptic encephalopathy, 4 early myoclonic encephalopathy epilepsy intellectual disability Neurodevelopmental Disorders large cell medulloblastoma malignant colon neoplasm medulloblastoma astrocytic tumor oligodendroglioma pancreatitis primitive neuroectodermal tumor ductal breast carcinoma in situ subependymal giant cell astrocytoma West syndrome developmental and epileptic encephalopathy, 4 early myoclonic encephalopathy epilepsy intellectual disability Neurodevelopmental Disorders large cell medulloblastoma malignant colon neoplasm medulloblastoma astrocytic tumor oligodendroglioma pancreatitis primitive neuroectodermal tumor ductal breast carcinoma in situ subependymal giant cell astrocytoma West syndrome familial infantile myoclonic epilepsy Lennox-Gastaut syndrome malignant ependymoma atypical Rett syndrome ovarian cancer Crohn disease Pick disease developmental and epileptic encephalopathy, 6 psoriasis glioblastoma invasive ductal breast carcinoma lung cancer malignant glioma non-small cell lung carcinoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia developmental and epileptic encephalopathy pilocytic astrocytoma Dravet syndrome schizophrenia ulcerative colitis
A	Pharos: P43378	atypical teratoid rhabdoid tumor malignant glioma psoriasis glioblastoma Pick disease large cell medulloblastoma progressive supranuclear palsy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth F]	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

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.