6F28 | pdb_00006f28

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2'-Amino-2'-carboxyethyl]-6-methyl-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.4A

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)
A	d6f28a_	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	d6f28b_	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e6f28A1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: NMT	F:	ECOD (20:10:01)
A		e6f28A2	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: Ephrin_lbd	F:	ECOD (20:10:01)
B		e6f28B1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: Glyco_transf_4	F:	ECOD (20:10:01)
B		e6f28B2	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: Ephrin_lbd	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
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, B	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, B	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, B	Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3	glutamate receptor activity G protein-coupled glutamate receptor activity molecular transducer activity adenylate cyclase inhibiting G protein-coupled glutamate receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential monoatomic ion channel activity channel activity glutamate receptor activity G protein-coupled glutamate receptor activity molecular transducer activity adenylate cyclase inhibiting G protein-coupled glutamate receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity transmitter-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate-gated calcium ion channel activity carboxylic acid transmembrane transporter activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity monoatomic cation channel activity calcium ion transmembrane transporter activity transmitter-gated channel activity metal ion transmembrane transporter activity 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 regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation glutamate receptor signaling pathway cell communication cellular process signal transduction trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation glutamate receptor signaling pathway cell communication cellular process signal transduction trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality regulation of membrane potential 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 G protein-coupled glutamate receptor signaling pathway G protein-coupled receptor signaling pathway	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 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 axon neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton neuron projection terminus presynaptic membrane dendrite dendritic tree glutamatergic synapse neuron projection cytoplasm intracellular anatomical structure dendrite cytoplasm cytoplasm cochlear hair cell ribbon synapse ribbon synapse

InterPro: Protein Family Classification InterPro Database Homepage

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

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.