5NIH | pdb_00005nih

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist LM-12b at 1.3 A resolution.

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d5niha1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth A]	d5niha2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A [auth B]	d5nihb_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	Phage_integrase	e5nihA1	A: a/b three-layered sandwiches	X: Carbon-nitrogen hydrolase-like	H: SSHS domain in CRISPR-associated endonuclease Cas9	T: SSHS domain in CRISPR-associated endonuclease Cas9	F: Phage_integrase	ECOD (v294.1)
A [auth B]	Phage_integrase	e5nihB1	A: a/b three-layered sandwiches	X: Carbon-nitrogen hydrolase-like	H: SSHS domain in CRISPR-associated endonuclease Cas9	T: SSHS domain in CRISPR-associated endonuclease Cas9	F: Phage_integrase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A [auth B], B [auth A]	PF10613	Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)	Ligated ion channel L-glutamate- and glycine-binding site	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF ...	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF00060.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A]	Glutamate receptor 2	transmitter-gated monoatomic ion channel activity glutamate receptor activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity passive transmembrane transporter activity transmitter-gated monoatomic ion channel activity glutamate receptor activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity passive transmembrane transporter activity channel activity transmembrane signaling receptor activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity amyloid-beta binding binding peptide binding cytoskeletal protein binding protein binding excitatory extracellular ligand-gated monoatomic ion channel activity extracellularly glutamate-gated ion channel activity protein-containing complex binding immunoglobulin binding identical protein binding monoatomic cation transmembrane transporter activity monoatomic cation channel activity ligand-gated monoatomic cation channel activity PDZ domain binding protein domain specific binding signaling receptor binding glutamate receptor binding ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential scaffold protein binding ligand-gated calcium channel activity calcium channel activity glutamate-gated calcium ion channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity ionotropic glutamate receptor binding SNARE binding kinase binding enzyme binding protein kinase binding transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential sodium channel activity kainate selective glutamate receptor activity potassium ion transmembrane transporter activity ligand-gated sodium channel activity sodium ion transmembrane transporter activity potassium channel activity	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 membrane organization cellular localization postsynapse organization AMPA glutamate receptor clustering glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane cellular component organization localization cell junction organization receptor clustering macromolecule localization cellular component organization or biogenesis synapse organization intracellular protein localization postsynaptic membrane organization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor response to lithium ion response to metal ion response to chemical 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 behavior learning learning or memory cognition conditioned place preference associative learning regulation of receptor recycling regulation of macromolecule metabolic process receptor recycling receptor metabolic process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to amine stimulus cellular response to nitrogen compound response to amine cellular response to chemical stimulus response to nitrogen compound positive regulation of synaptic transmission establishment of protein localization response to antibiotic response to fungicide response to toxic substance cellular response to acid chemical cellular response to amino acid stimulus response to glycine response to oxygen-containing compound response to amino acid cellular response to glycine cellular response to oxygen-containing compound response to acid chemical ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway negative regulation of signaling negative regulation of biological process negative regulation of synaptic transmission negative regulation of cell communication negative regulation of cellular process regulation of synaptic plasticity long-term synaptic depression regulation of long-term synaptic depression synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic 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 somatodendritic compartment cell body perikaryon neuronal cell body cell surface external side of plasma membrane side of membrane 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 presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection glutamatergic synapse extracellular region perisynaptic space spine synapse dendritic shaft neuron spine dendritic spine membrane-bounded organelle intracellular anatomical structure intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane secretory vesicle cytoplasm organelle membrane exocytic vesicle axon dendritic spine neck axon terminus distal axon terminal bouton neuron projection terminus dendritic spine head growth cone site of polarized growth neuron projection cytoplasm dendrite cytoplasm dendritic spine cytoplasm presynaptic active zone membrane presynaptic active zone cell leading edge leading edge membrane neuron projection membrane dendrite membrane cell projection membrane excitatory synapse Schaffer collateral - CA1 synapse endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A [auth B], B [auth A]	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A [auth B], B [auth A]	IPR001828	Receptor, ligand binding region	Domain
A [auth B], B [auth A]	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A [auth B], B [auth A]	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A [auth B], B [auth A]	IPR015683	Ionotropic glutamate receptor	Family

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.