3NFL | pdb_00003nfl

Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3nfla_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Tyrosine-protein phosphatase non-receptor type 4, PTPN4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3nflb_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Tyrosine-protein phosphatase non-receptor type 4, PTPN4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3nflc_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Tyrosine-protein phosphatase non-receptor type 4, PTPN4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3nfld_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Tyrosine-protein phosphatase non-receptor type 4, PTPN4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PDZ domain-like	8039244	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8039244	3000388	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PDZ domain-like	8039244	3000388	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PDZ domain-like	8039244	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)
A	PDZ	e3nflA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
B	PDZ	e3nflB1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
C	PDZ	e3nflC1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
D	PDZ	e3nflD1	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Glutamate [NMDA] receptor subunit epsilon-1	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel activity transmembrane transporter activity amide binding amyloid-beta binding binding peptide binding monoatomic cation transmembrane transporter activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate-gated calcium ion channel activity monoatomic cation channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential postsynaptic neurotransmitter receptor activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction 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 positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process glutamate receptor signaling pathway behavior learning or memory cognition memory amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process dopamine metabolic process catechol-containing compound metabolic process biogenic amine metabolic process transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse localization within membrane protein localization to membrane macromolecule localization protein localization to postsynapse intracellular protein localization protein localization to cell junction startle response neuromuscular process response to external stimulus regulation of neuronal synaptic plasticity regulation of synaptic plasticity response to stress response to wounding negative regulation of biological process negative regulation of protein catabolic process regulation of primary metabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of metabolic process regulation of protein catabolic process neurogenesis cellular developmental process cell differentiation synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic regulation of localization regulation of transport regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport response to light stimulus learning visual learning visual behavior associative learning response to radiation response to abiotic stimulus serotonin metabolic process indole-containing compound metabolic process response to alcohol response to oxygen-containing compound response to ethanol sodium ion transmembrane transport sodium ion transport sleep directional locomotion locomotion calcium ion transmembrane import into cytosol ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway response to amine response to nitrogen compound response to amphetamine excitatory chemical synaptic transmission sensory perception sensory perception of pain long-term synaptic potentiation	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 presynapse presynaptic membrane glutamatergic synapse neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle synaptic vesicle secretory vesicle cytoplasm vesicle exocytic vesicle protein-containing complex plasma membrane protein complex membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex cell surface organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cytoplasmic vesicle membrane vesicle membrane
A, B, C, D	Tyrosine-protein phosphatase non-receptor type 4	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 cytoskeletal protein binding protein binding binding signaling receptor binding glutamate receptor binding	protein dephosphorylation dephosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoskeleton membraneless organelle intracellular membraneless organelle cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR018884	Glutamate [NMDA] receptor, epsilon subunit, C-terminal	Domain
E, F, G, H	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
E, F, G, H	IPR001508	Ionotropic glutamate receptor, metazoa	Family
E, F, G, H	IPR001828	Receptor, ligand binding region	Domain
E, F, G, H	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
E, F, G, H	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
E, F, G, H	IPR015683	Ionotropic glutamate receptor	Family
A, B, C, D	IPR000299	FERM domain	Domain
A, B, C, D	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A, B, C, D	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B, C, D	IPR019748	FERM central domain	Domain
A, B, C, D	IPR018980	FERM, C-terminal PH-like domain	Domain
A, B, C, D	IPR012151	Protein-tyrosine phosphatase, non-receptor type-3, -4	Family
A, B, C, D	IPR041783	PTPN3/4, FERM domain C-lobe	Domain
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR014847	FERM adjacent	Domain
A, B, C, D	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B, C, D	IPR019749	Band 4.1 domain	Domain
A, B, C, D	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B, C, D	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A, B, C, D	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B, C, D	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C, D	IPR019747	FERM conserved site	Conserved Site
A, B, C, D	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A, B, C, D	IPR018979	FERM, N-terminal	Domain
A, B, C, D	IPR001478	PDZ domain	Domain
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: Q12879	Landau-Kleffner syndrome epilepsy rolandic epilepsy melanoma autism colorectal cancer morphine dependence schizophrenia substance withdrawal syndrome bipolar disorder speech disorder Language Development Disorders depressive disorder oligodendroglioma Parkinson disease Landau-Kleffner syndrome epilepsy rolandic epilepsy melanoma autism colorectal cancer morphine dependence schizophrenia substance withdrawal syndrome bipolar disorder speech disorder Language Development Disorders depressive disorder oligodendroglioma Parkinson disease pilocytic astrocytoma psoriasis subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor large cell medulloblastoma lung carcinoma medulloblastoma continuous spikes and waves during sleep opiate dependence postencephalitic Parkinson disease glioblastoma astrocytic tumor auditory perceptual disorders Lennox-Gastaut syndrome autism spectrum disorder malignant ependymoma colorectal carcinoma cutaneous melanoma neurodegenerative disease ovarian cancer Pick disease primitive neuroectodermal tumor hepatitis B virus infection intellectual disability attention deficit hyperactivity disorder, inattentive type toxic encephalopathy malignant glioma
A, B, C, D	Pharos: P29074	astrocytic tumor gastric carcinoma large cell medulloblastoma malignant mesothelioma osteosarcoma pilocytic astrocytoma atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma medulloblastoma ovarian cancer primitive neuroectodermal tumor gastric cancer hepatocellular carcinoma malignant glioma astrocytic tumor gastric carcinoma large cell medulloblastoma malignant mesothelioma osteosarcoma pilocytic astrocytoma atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma medulloblastoma ovarian cancer primitive neuroectodermal tumor gastric cancer hepatocellular carcinoma malignant glioma oligodendroglioma Pick disease