9B37

Open state of kainate receptor GluK2 in complex with agonist glutamate and positive allosteric modulator BPAM344 bound to one concanavalin A dimer. Composite map.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2021-05-27)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8073922	3000120	SCOP2B (2021-05-27)
F	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8073922	3000120	SCOP2B (2021-05-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, B, C, D	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family
A, B, C, D	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
E, F	PF00139	Legume lectin domain (Lectin_legB)	Legume lectin domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glutamate receptor ionotropic, kainate 2	gated channel activity monoatomic ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity extracellularly glutamate-gated ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity ubiquitin protein ligase binding protein binding gated channel activity monoatomic ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity extracellularly glutamate-gated ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding PDZ domain binding protein domain specific binding glutamate receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential scaffold protein binding ubiquitin-like protein conjugating enzyme binding ubiquitin conjugating enzyme binding SNARE binding transmitter-gated monoatomic ion channel activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity amino acid transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity organic anion 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 monoatomic cation transmembrane transporter activity sodium channel activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity ligand-gated monoatomic cation 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 monoatomic cation channel activity metal ion transmembrane transporter activity	cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process response to stimulus signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process response to stimulus signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality 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 regulation of JNK cascade regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction JNK cascade intracellular signaling cassette MAPK cascade presynaptic modulation of chemical synaptic transmission detection of external stimulus thermoception detection of cold stimulus involved in thermoception response to external stimulus sensory perception of temperature stimulus detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of temperature stimulus involved in thermoception sensory perception of cold stimulus detection of temperature stimulus response to abiotic stimulus detection of stimulus involved in sensory perception neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of long-term neuronal synaptic plasticity negative regulation of signaling synaptic transmission, glutamatergic negative regulation of biological process regulation of synaptic transmission, glutamatergic negative regulation of synaptic transmission negative regulation of cell communication negative regulation of cellular process negative regulation of synaptic transmission, glutamatergic inhibitory postsynaptic potential protein localization localization cellular localization receptor clustering cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane positive regulation of cell communication positive regulation of synaptic transmission positive regulation of signaling negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process regulation of short-term neuronal synaptic plasticity action potential transmission of nerve impulse neuronal action potential behavioral defense response behavior fear response behavioral fear response defense response response to stress multicellular organismal response to stress	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 somatodendritic compartment cell body perikaryon neuronal cell body protein-containing complex sodium channel complex plasma membrane protein complex membrane protein complex potassium channel complex cation channel complex transporter complex kainate selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex transmembrane transporter complex neurotransmitter receptor 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 axon axon terminus distal axon terminal bouton neuron projection terminus mossy fiber rosette neuron projection cytoplasm intracellular anatomical structure cytoplasmic region plasma membrane bounded cell projection cytoplasm dendrite cytoplasm cytoplasm hippocampal mossy fiber to CA3 synapse
E, F	Concanavalin A	binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding calcium ion binding D-glucose binding	regulation of tube diameter multicellular organismal process system process regulation of tube size biological regulation circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality vasodilation blood circulation regulation of anatomical structure size	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, B, C, D	IPR001828	Receptor, ligand binding region	Domain
A, B, C, D	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B, C, D	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, B, C, D	IPR015683	Ionotropic glutamate receptor	Family
E, F	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
E, F	IPR001220	Legume lectin domain	Domain
E, F	IPR000985	Legume lectin, alpha chain, conserved site	Conserved Site
E, F	IPR019825	Legume lectin, beta chain, Mn/Ca-binding site	Binding Site

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

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 R01GM133198.