3I4W

Crystal Structure of the third PDZ domain of PSD-95

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3i4wa_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3i4wb_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3i4wc_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3i4wd_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PDZ	e3i4wA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
B	PDZ	e3i4wB1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
C	PDZ	e3i4wC1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
D	PDZ	e3i4wD1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
C	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
D	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
A, B, C, D	PF10600	PDZ-associated domain of NMDA receptors (PDZ_assoc)	PDZ-associated domain of NMDA receptors	This domain is found in higher eukaryotes between the second and third PDZ domains, Pfam:PF00595, of glutamate receptor like proteins. Its exact function is not known.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Disks large homolog 4	protein phosphatase binding phosphatase binding protein binding binding enzyme binding protein-containing complex binding D1 dopamine receptor binding signaling receptor binding G protein-coupled receptor binding dopamine receptor binding PDZ domain binding protein domain specific binding scaffold protein binding ionotropic glutamate receptor binding protein phosphatase binding phosphatase binding protein binding binding enzyme binding protein-containing complex binding D1 dopamine receptor binding signaling receptor binding G protein-coupled receptor binding dopamine receptor binding PDZ domain binding protein domain specific binding scaffold protein binding ionotropic glutamate receptor binding glutamate receptor binding kinase binding acetylcholine receptor binding adrenergic receptor binding beta-1 adrenergic receptor binding neuroligin family protein binding P2Y1 nucleotide receptor binding G protein-coupled nucleotide receptor binding	protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery 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 protein localization to organelle cellular macromolecule localization protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery 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 protein localization to organelle cellular macromolecule localization macromolecule localization cellular process protein localization to postsynapse 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 membrane organization postsynapse organization AMPA glutamate receptor clustering glutamate receptor clustering neurotransmitter-gated ion channel clustering cellular component organization cell junction organization receptor clustering cellular component organization or biogenesis synapse organization postsynaptic membrane organization behavior learning learning or memory cognition neurotransmitter receptor diffusion trapping receptor diffusion trapping postsynaptic neurotransmitter receptor diffusion trapping cellular response to inorganic substance cellular response to metal ion response to potassium ion response to inorganic substance cellular response to chemical stimulus response to metal ion response to chemical cellular response to potassium ion regulation of localization import into cell regulation of cellular component organization 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 positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process primary metabolic process regulation of cellular metabolic process regulation of molecular function positive regulation of kinase activity regulation of protein tyrosine kinase activity regulation of kinase activity macromolecule modification metabolic process regulation of phosphorus metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of molecular function positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation organic substance metabolic process protein metabolic process positive regulation of protein kinase activity organonitrogen compound metabolic process positive regulation of transferase activity positive regulation of protein tyrosine kinase activity regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity regulation of macromolecule metabolic process regulation of protein kinase activity regulation of phosphorylation peptidyl-tyrosine phosphorylation regulation of 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 multicellular organism development anatomical structure development nervous system development system development 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 dendrite development cell differentiation dendritic spine morphogenesis dendritic spine development plasma membrane bounded cell projection organization dendritic spine organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development neuron projection organization positive regulation of cellular component organization 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 establishment of protein localization regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of transporter activity regulation of NMDA receptor activity regulation of monoatomic ion transmembrane transporter activity transmembrane transport regulation of transmembrane transport regulation of neurotransmitter receptor activity neuromuscular process neuromuscular process controlling balance locomotory behavior exploration behavior locomotory exploration behavior biological process involved in intraspecies interaction between organisms social behavior cell adhesion cell-cell adhesion vocalization behavior vesicle organization synaptic vesicle maturation organelle organization developmental maturation establishment or maintenance of bipolar cell polarity establishment or maintenance of epithelial cell apical/basal polarity establishment or maintenance of apical/basal cell polarity establishment or maintenance of cell polarity	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region axon cell projection main axon juxtaparanode region of axon neuron projection plasma membrane bounded cell projection 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 intracellular anatomical structure cytoplasm cytosol basal part of cell basal plasma membrane basolateral plasma membrane glutamatergic synapse cell-cell junction adherens junction anchoring junction neuromuscular junction membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle organelle membrane endocytic vesicle neuron spine dendritic spine somatodendritic compartment dendrite dendritic tree extrinsic component of plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane side of membrane transport vesicle endomembrane system presynapse synaptic vesicle secretory vesicle exocytic vesicle cell cortex cortical cytoskeleton cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle neuron projection cytoplasm cytoplasmic region plasma membrane bounded cell 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
A, B, C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR020590	Guanylate kinase, conserved site	Conserved Site
A, B, C, D	IPR019583	Disks large homolog 1-4, PDZ-associated domain	Domain
A, B, C, D	IPR016313	Disks large 1-like	Family
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR001452	SH3 domain	Domain
A, B, C, D	IPR019590	Disks large homologue 1, N-terminal PEST domain	Domain
A, B, C, D	IPR008144	Guanylate kinase-like domain	Domain
A, B, C, D	IPR008145	Guanylate kinase/L-type calcium channel beta subunit	Domain
A, B, C, D	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C, D	IPR001478	PDZ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P78352	polycystic ovary syndrome Williams syndrome Neurodevelopmental Disorders schizophrenia intellectual disability malignant glioma oligodendroglioma Pick disease Alzheimer disease primitive neuroectodermal tumor atypical teratoid rhabdoid tumor depressive disorder fragile X syndrome juvenile dermatomyositis major depressive disorder polycystic ovary syndrome Williams syndrome Neurodevelopmental Disorders schizophrenia intellectual disability malignant glioma oligodendroglioma Pick disease Alzheimer disease primitive neuroectodermal tumor atypical teratoid rhabdoid tumor depressive disorder fragile X syndrome juvenile dermatomyositis major depressive disorder malignant pancreatic neoplasm osteosarcoma pilocytic astrocytoma amyotrophic lateral sclerosis psoriasis autism subependymal giant cell astrocytoma vascular disease bipolar disorder Emery-Dreifuss muscular dystrophy glioblastoma large cell medulloblastoma malignant ependymoma medulloblastoma ovarian cancer astrocytic tumor autism spectrum disorder toxic encephalopathy dementia exocrine pancreatic carcinoma lung carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	SNN	Parent Component: ASN RESID: AA0302 , AA0593 PSI-MOD : L-aspartimide MOD:00307 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asn) MOD:01940 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asp) MOD:01941

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.