5KC9 | pdb_00005kc9

Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-1 (GluD1)

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)
C	d5kc9c_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	House mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5kc9b_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	House mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5kc9a_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	House mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Glyco_hydro_18	e5kc9C1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Glyco_hydro_18	ECOD (develop294)
B	Glyco_hydro_18	e5kc9B1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Glyco_hydro_18	ECOD (develop294)
A	XRCC4	e5kc9A1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Glutamate receptor ionotropic, delta-1	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 G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential G protein-coupled receptor activity GABA receptor activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	regulation of postsynaptic membrane neurotransmitter receptor levels biological regulation regulation of biological quality regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling negative regulation of synaptic plasticity cell-cell signaling chemical synaptic transmission cell communication regulation of postsynaptic membrane neurotransmitter receptor levels biological regulation regulation of biological quality regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling negative regulation of synaptic plasticity cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular process synaptic signaling via neuropeptide cellular response to stimulus response to stimulus phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction behavior multicellular organismal process biological process involved in intraspecies interaction between organisms social behavior regulation of cellular component organization postsynapse organization regulation of postsynapse organization cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization cellular component organization or biogenesis synaptic transmission, glutamatergic	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 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 GABA-ergic synapse glutamatergic synapse trans-synaptic protein complex neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree

InterPro: Protein Family Classification InterPro Database Homepage

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