6NID | pdb_00006nid

Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	PDZ domain-like	8041734	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8041734	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PDZ domain-like	8041734	3000388	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)
C	MG4	e6nidC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (v294.1)
B	MG4	e6nidB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (v294.1)
A	MG4	e6nidA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (utative)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (utative)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	Neurexin-1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity cell adhesion molecule binding protein binding channel regulator activity ion channel regulator activity calcium channel regulator activity molecular function regulator activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity cell adhesion molecule binding protein binding channel regulator activity ion channel regulator activity calcium channel regulator activity molecular function regulator activity transporter regulator activity signaling receptor binding acetylcholine receptor binding neuroligin family 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 behavior learning learning or memory cognition positive regulation of nervous system development positive regulation of cellular component organization regulation of cellular component organization regulation of developmental 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 synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly system development developmental process regulation of multicellular organismal development positive regulation of cellular component biogenesis 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 synapse assembly positive regulation of synapse assembly imitative learning auditory behavior vocal learning learned vocalization behavior or vocal learning response to mechanical stimulus response to external stimulus mechanosensory behavior response to auditory stimulus observational learning response to abiotic stimulus developmental maturation synapse maturation regulation of synapse maturation positive regulation of synapse maturation synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic cellular localization neurotransmitter secretion transport secretion export from cell neurotransmitter transport establishment of localization localization signal release from synapse secretion by cell signal release establishment of localization in cell postsynaptic membrane assembly membrane biogenesis receptor clustering intracellular protein localization postsynaptic membrane organization membrane organization postsynapse organization postsynapse assembly neuroligin clustering involved in postsynaptic membrane assembly localization within membrane protein localization to membrane membrane assembly macromolecule localization adult behavior neuromuscular process neuromuscular process controlling balance organelle organization postsynaptic density protein 95 clustering postsynaptic density organization postsynaptic specialization organization cell adhesion cell-cell adhesion neuron cell-cell adhesion axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development biological process involved in intraspecies interaction between organisms social behavior vocalization behavior protein localization to synapse organelle assembly postsynaptic specialization assembly excitatory synapse assembly gephyrin clustering involved in postsynaptic density assembly protein localization to cell junction postsynaptic density assembly	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen vesicle nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cell surface cell periphery plasma membrane presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane somatodendritic compartment cell body neuronal cell body endoplasmic reticulum cytoplasm
A, B, C	Peripheral plasma membrane protein CASK	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 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 nucleobase-containing compound kinase activity nucleoside monophosphate kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor GMP kinase activity transferase activity, transferring phosphorus-containing groups protein binding calmodulin binding signaling receptor binding neurexin family protein binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor protein serine/threonine kinase activity	regulation of biological process cellular response to growth factor stimulus response to stimulus negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of biological process negative regulation of cellular response to growth factor stimulus cellular response to endogenous stimulus regulation of response to stimulus response to growth factor wound healing regulation of response to external stimulus regulation of biological process cellular response to growth factor stimulus response to stimulus negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of biological process negative regulation of cellular response to growth factor stimulus cellular response to endogenous stimulus regulation of response to stimulus response to growth factor wound healing regulation of response to external stimulus negative regulation of wound healing response to external stimulus negative regulation of response to wounding regulation of response to wounding response to stress regulation of response to stress negative regulation of response to external stimulus regulation of wound healing response to wounding regulation of localization cellular localization regulation of cellular process transport modulation of chemical synaptic transmission signaling cell communication localization synaptic signaling regulation of secretion by cell secretion by cell signal release establishment of localization in cell trans-synaptic signaling regulation of signaling neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport export from cell cell-cell signaling neurotransmitter transport establishment of localization regulation of secretion chemical synaptic transmission signal release from synapse regulation of trans-synaptic signaling regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of cell communication cellular process regulation of calcium ion import regulation of calcium ion transport positive regulation of calcium ion transport positive regulation of calcium ion import regulation of monoatomic ion transport positive regulation of biological process calcium ion transport metal ion transport positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport cell adhesion negative regulation of cell population proliferation cell population proliferation regulation of keratinocyte proliferation negative regulation of keratinocyte proliferation regulation of cell population proliferation negative regulation of cellular process regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation keratinocyte proliferation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport vesicle-mediated transport in synapse regulation of regulated secretory pathway regulation of synaptic vesicle exocytosis regulation of vesicle-mediated transport exocytosis regulation of exocytosis regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion negative regulation of cell-matrix adhesion negative regulation of cell adhesion cell-matrix adhesion regulation of cell-matrix adhesion negative regulation of cell-substrate adhesion macromolecule localization intracellular protein localization	cell-cell junction cellular anatomical structure anchoring junction cell junction basement membrane extracellular matrix external encapsulating structure extracellular region intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cell-cell junction cellular anatomical structure anchoring junction cell junction basement membrane extracellular matrix external encapsulating structure extracellular region intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol cell periphery presynapse synapse membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane basal part of cell basal plasma membrane basolateral plasma membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix focal adhesion cell-substrate junction nucleolus vesicle cilium ciliary membrane plasma membrane bounded cell projection cell projection bounding membrane of organelle organelle membrane cell projection membrane endomembrane system organelle envelope nuclear envelope nuclear periphery nuclear lamina Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR050372	Neurexin-related cell adhesion and synaptic protein	Family
D, E, F	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
D, E, F	IPR000742	EGF-like domain	Domain
D, E, F	IPR001791	Laminin G domain	Domain
D, E, F	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
D, E, F	IPR003585	Neurexin/syndecan/glycophorin C	Domain
A, B, C	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C	IPR000719	Protein kinase domain	Domain
A, B, C	IPR020590	Guanylate kinase, conserved site	Conserved Site
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C	IPR001452	SH3 domain	Domain
A, B, C	IPR008144	Guanylate kinase-like domain	Domain
A, B, C	IPR035473	CASK, SH3 domain	Domain
A, B, C	IPR008145	Guanylate kinase/L-type calcium channel beta subunit	Domain
A, B, C	IPR004172	L27 domain	Domain
A, B, C	IPR014775	L27 domain, C-terminal	Domain
A, B, C	IPR050716	Membrane-associated guanylate kinase	Family
A, B, C	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C	IPR036892	L27 domain superfamily	Homologous Superfamily
A, B, C	IPR001478	PDZ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, E, F	Pharos: Q9ULB1	Pitt-Hopkins-like syndrome 2 intellectual disability schizophrenia chromosome 2P16.3 deletion syndrome Pitt-Hopkins syndrome Language Development Disorders autism autism spectrum disorder malignant colon neoplasm medulloblastoma oligodendroglioma attention deficit hyperactivity disorder, inattentive type Pick disease subependymal giant cell astrocytoma endogenous depression Pitt-Hopkins-like syndrome 2 intellectual disability schizophrenia chromosome 2P16.3 deletion syndrome Pitt-Hopkins syndrome Language Development Disorders autism autism spectrum disorder malignant colon neoplasm medulloblastoma oligodendroglioma attention deficit hyperactivity disorder, inattentive type Pick disease subependymal giant cell astrocytoma endogenous depression large cell medulloblastoma malignant ependymoma Alzheimer disease ovarian cancer atypical teratoid rhabdoid tumor pilocytic astrocytoma pituitary cancer psoriasis bipolar disorder lung carcinoma malignant glioma nasopharyngeal carcinoma astrocytic tumor pancreatic intraductal papillary-mucinous carcinoma auditory perceptual disorders primitive neuroectodermal tumor breast cancer depressive disorder glioblastoma
A, B, C	Pharos: O14936	FG syndrome syndromic X-linked intellectual disability Najm type microcephaly cleft palate sarcomatoid carcinoma cerebellar disease FG syndrome 4 intellectual disability Mammary Neoplasms, Experimental carcinoma FG syndrome 3 glioblastoma undifferentiated carcinoma large cell medulloblastoma malignant ependymoma FG syndrome syndromic X-linked intellectual disability Najm type microcephaly cleft palate sarcomatoid carcinoma cerebellar disease FG syndrome 4 intellectual disability Mammary Neoplasms, Experimental carcinoma FG syndrome 3 glioblastoma undifferentiated carcinoma large cell medulloblastoma malignant ependymoma mammary neoplasms, animal astrocytic tumor autism, susceptibility to, X-linked 2 microlissencephaly non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia lung carcinoma malignant glioma nasopharyngeal carcinoma oligodendroglioma congenital nonspherocytic hemolytic anemia pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma FG syndrome 2 primitive neuroectodermal tumor invasive ductal breast carcinoma lung large cell carcinoma arthrogryposis medulloblastoma atypical teratoid rhabdoid tumor osteosarcoma developmental and epileptic encephalopathy pancreatic intraductal papillary-mucinous neoplasm esophageal adenocarcinoma pituitary cancer