5YPO | pdb_00005ypo

Crystal structure of PSD-95 GK domain in complex with phospho-SAPAP 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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058020	3002021	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058020	3002021	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)
B [auth A]		e5ypoA1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: F_bP_aldolase	F:	ECOD (20:10:01)
A [auth B]		e5ypoB1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: F_bP_aldolase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF00625	Guanylate kinase (Guanylate_kin)	Guanylate kinase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	SAPAP	molecular adaptor activity protein-containing complex binding binding	trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular process	postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse postsynaptic specialization organelle synapse cell junction asymmetric synapse cell periphery plasma membrane membrane glutamatergic synapse
A [auth B], B [auth A]	Disks large homolog 4	structural constituent of postsynapse structural molecule activity structural constituent of postsynaptic density structural constituent of synapse structural constituent of postsynaptic specialization beta-2 adrenergic receptor binding protein binding binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding frizzled binding protein phosphatase binding phosphatase binding structural constituent of postsynapse structural molecule activity structural constituent of postsynaptic density structural constituent of synapse structural constituent of postsynaptic specialization beta-2 adrenergic receptor binding protein binding binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding frizzled binding protein phosphatase binding phosphatase binding enzyme binding protein-containing complex binding D1 dopamine receptor binding dopamine receptor binding cytoskeletal protein binding kinesin binding PDZ domain binding protein domain specific binding glutamate receptor binding scaffold protein binding ionotropic glutamate receptor binding kinase binding acetylcholine receptor binding protein kinase binding beta-1 adrenergic receptor binding neuroligin family protein binding P2Y1 nucleotide receptor binding G protein-coupled nucleotide receptor binding	protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle cellular process protein localization to postsynapse intracellular protein localization regulation of biological quality protein localization to cell junction receptor localization to synapse 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 positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process 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 excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling positive regulation of AMPA glutamate receptor clustering regulation of localization regulation of postsynaptic membrane organization positive regulation of cellular component organization regulation of cellular component organization regulation of protein localization regulation of AMPA glutamate receptor clustering positive regulation of postsynaptic membrane organization cellular component organization receptor clustering cellular component organization or biogenesis synapse organization regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane membrane organization postsynapse organization positive regulation of receptor clustering AMPA glutamate receptor clustering positive regulation of protein localization to membrane glutamate receptor clustering neurotransmitter-gated ion channel clustering regulation of glutamate receptor clustering cell junction organization regulation of cellular localization positive regulation of protein localization cellular response to metal ion cellular response to chemical stimulus response to metal ion response to potassium ion response to chemical cellular response to potassium ion import into cell receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport negative regulation of cellular process regulation of endocytosis negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis negative regulation of receptor internalization regulation of behavior behavior regulation of grooming behavior grooming behavior regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of long-term neuronal synaptic plasticity developmental process head development forebrain development animal organ development brain development nervous system development pallium development cerebral cortex development multicellular organism development central nervous system development anatomical structure development telencephalon development system development dendritic spine organization plasma membrane bounded cell projection organization cell projection organization neuron projection organization cellular developmental process plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation dendritic spine morphogenesis dendritic spine development dendrite morphogenesis cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway NMDA selective glutamate receptor signaling pathway regulation of developmental process regulation of neuron projection arborization regulation of cell morphogenesis positive regulation of developmental process positive regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell projection organization positive regulation of neuron projection arborization neuron projection arborization positive regulation of synaptic transmission positive regulation of cytosolic calcium ion concentration cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly positive regulation of nervous system development regulation of nervous system development cell junction assembly regulation of synapse structure or activity 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 regulation of synapse organization positive regulation of multicellular organismal process synapse assembly positive regulation of synapse assembly establishment of protein localization regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of NMDA receptor activity transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of neurotransmitter receptor activity neuromuscular process neuromuscular process controlling balance locomotory behavior exploration behavior locomotory exploration behavior developmental maturation neuronal ion channel clustering anatomical structure maturation neuron maturation cell maturation biological process involved in intraspecies interaction between organisms social behavior cell adhesion cell-cell adhesion vocalization behavior regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of dendrite morphogenesis positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development regulation of neuron projection development positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of dendrite morphogenesis regulation of plasma membrane bounded cell projection organization vesicle organization synaptic vesicle maturation organelle organization	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 projection dendritic branch dendrite dendritic tree neuron projection plasma membrane bounded cell projection axon main axon juxtaparanode region of axon cell-cell junction anchoring junction protein-containing complex plasma membrane protein complex membrane protein complex transporter complex receptor complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex proximal dendrite intracellular anatomical structure cytoplasm cytosol glutamatergic synapse neuromuscular junction neuron spine dendritic spine membrane-bounded organelle transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle secretory vesicle vesicle exocytic vesicle cell cortex cortical cytoskeleton intracellular membraneless organelle cytoskeleton membraneless organelle neuron projection cytoplasm dendrite cytoplasm neuron projection terminus excitatory synapse cerebellar mossy fiber endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR005026	SAPAP family	Family
A [auth B], B [auth A]	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR020590	Guanylate kinase, conserved site	Conserved Site
A [auth B], B [auth A]	IPR019583	Disks large homolog 1-4, PDZ-associated domain	Domain
A [auth B], B [auth A]	IPR016313	Disks large 1-like	Family
A [auth B], B [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B], B [auth A]	IPR050614	Synaptic Scaffolding LAP/MAGUK Families	Family
A [auth B], B [auth A]	IPR001452	SH3 domain	Domain
A [auth B], B [auth A]	IPR019590	Disks large homologue 1, N-terminal PEST domain	Domain
A [auth B], B [auth A]	IPR008144	Guanylate kinase-like domain	Domain
A [auth B], B [auth A]	IPR008145	Guanylate kinase/L-type calcium channel beta subunit	Domain
A [auth B], B [auth A]	IPR036034	PDZ superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR001478	PDZ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: O14490	Neurodevelopmental Disorders adrenal cortex carcinoma endometriosis lung carcinoma malignant mesothelioma oligodendroglioma primitive neuroectodermal tumor astrocytic tumor glioblastoma malignant ependymoma medulloblastoma ovarian cancer schizophrenia atypical teratoid rhabdoid tumor large cell medulloblastoma Neurodevelopmental Disorders adrenal cortex carcinoma endometriosis lung carcinoma malignant mesothelioma oligodendroglioma primitive neuroectodermal tumor astrocytic tumor glioblastoma malignant ependymoma medulloblastoma ovarian cancer schizophrenia atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma pilocytic astrocytoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.