5NEB

Structure of GluK1 ligand-binding domain (S1S2) in complex with LM-12b at 2.05 A resolution

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d5nebb1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A [auth B]	d5nebb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth A]	d5neba1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth A]	d5neba2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Rat (Rattus norvegicus ) [TaxId: 10116 ], Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Type 2 solute binding protein-like	8040517	3000083	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Type 2 solute binding protein-like	8040517	3000083	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 [auth B]	Lig_chan_1	e5nebB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lig_chan_1	ECOD (1.6)
A [auth B]	Lig_chan_2	e5nebB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lig_chan_2	ECOD (1.6)
B [auth A]	Lig_chan_1	e5nebA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lig_chan_1	ECOD (1.6)
B [auth A]	Lig_chan_2	e5nebA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lig_chan_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B [auth A]	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 ionotropic, kainate 1	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 identical protein 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 identical protein binding protein binding binding L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity acidic amino acid transmembrane transporter activity L-glutamate transmembrane transporter activity carboxylic acid transmembrane transporter activity organic acid transmembrane transporter activity organic anion transmembrane transporter activity ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential scaffold protein binding monoatomic cation transmembrane transporter activity transmitter-gated monoatomic ion channel activity molecular transducer activity glutamate-gated receptor activity neurotransmitter receptor activity inorganic molecular entity transmembrane transporter activity ligand-gated calcium channel activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate receptor activity glutamate-gated calcium ion channel activity signaling receptor activity monoatomic cation channel activity calcium ion transmembrane transporter activity transmitter-gated channel activity metal ion transmembrane transporter activity SNARE binding 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 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 organic acid binding ion binding anion binding amino acid binding carboxylic acid binding glutamate binding small molecule binding	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 transport monoatomic ion transmembrane transport potassium ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport potassium ion transport monoatomic cation transport presynaptic modulation of chemical synaptic transmission amino acid transport amino acid transmembrane transport behavior response to stress multicellular organismal response to stress response to pain behavioral response to pain developmental process multicellular organism development anatomical structure development nervous system development system development 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 negative regulation of synaptic transmission, GABAergic synaptic transmission, GABAergic regulation of synaptic transmission, GABAergic positive regulation of cell communication positive regulation of synaptic transmission, GABAergic positive regulation of biological process positive regulation of cellular process positive regulation of synaptic transmission positive regulation of signaling adult behavior nitrogen compound transport organic anion transport gamma-aminobutyric acid secretion carboxylic acid transport secretion acid secretion organic acid transport gamma-aminobutyric acid transport regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of short-term neuronal synaptic plasticity cellular localization establishment of localization in cell sodium ion transmembrane transport sodium ion transport ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway regulation of localization positive regulation of amine transport positive regulation of secretion regulation of amino acid transport regulation of transport regulation of gamma-aminobutyric acid secretion positive regulation of gamma-aminobutyric acid secretion regulation of secretion positive regulation of organic acid transport amine transport positive regulation of transport positive regulation of amino acid transport regulation of organic acid transport regulation of amine transport membrane depolarization	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 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 somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection glutamatergic synapse cell body neuronal cell body axon axon terminus distal axon terminal bouton neuron projection terminus

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.