Annotations: 5VHY

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	8036483	3000083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	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	Amidase_2	e5vhyA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Amidase_2	ECOD (v294.1)
C	Amidase_2	e5vhyC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Amidase_2	ECOD (v294.1)
F	Amdase	e5vhyF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Amdase	ECOD (v294.1)
E	Amdase	e5vhyE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Amdase	ECOD (v294.1)
D	Amidase_2	e5vhyD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Amidase_2	ECOD (v294.1)
B	Amidase_2	e5vhyB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Amidase_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, B, C, D, E A, B, C, D, E, F	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
A, B, C, D, E A, B, C, D, E, F	PF07803	GSG1-like protein (GSG-1)	GSG1-like protein	-	Family
A, B, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	Glutamate receptor 2,Germ cell-specific gene 1-like protein	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	multicellular organismal process system process nervous system process cellular process transmission of nerve impulse cell communication cellular component organization cell junction organization synapse organization cellular component organization or biogenesis cellular response to stimulus regulation of localization regulation of cellular process response to stimulus multicellular organismal process system process nervous system process cellular process transmission of nerve impulse cell communication cellular component organization cell junction organization synapse organization cellular component organization or biogenesis cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport regulation of signaling receptor activity regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of signal transduction localization signal transduction regulation of biological process regulation of signaling regulation of transport biological regulation establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of response to stimulus regulation of neurotransmitter receptor activity regulation of cell communication regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of short-term neuronal synaptic plasticity modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of biological quality import into cell cellular localization regulation of cellular component organization receptor internalization postsynaptic neurotransmitter receptor internalization regulation of receptor internalization vesicle-mediated transport vesicle-mediated transport in synapse establishment of localization in cell regulation of postsynaptic neurotransmitter receptor internalization regulation of endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis endocytosis receptor-mediated endocytosis positive regulation of cell communication regulation of postsynaptic membrane potential positive regulation of signal transduction regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process chemical synaptic transmission, postsynaptic positive regulation of response to stimulus modulation of excitatory postsynaptic potential regulation of multicellular organismal process positive regulation of cellular process cell surface receptor signaling pathway regulation of nervous system process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling membrane organization postsynapse organization AMPA glutamate receptor clustering glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane receptor clustering macromolecule localization intracellular protein localization postsynaptic membrane organization 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 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 Schaffer collateral - CA1 synapse glutamatergic synapse 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 AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection 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 endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR012478	GSG1-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR050579	Peripheral myelin protein 22/Epithelial membrane protein-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, B, C, D, E A, B, C, D, E, F	IPR001828	Receptor, ligand binding region	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015683	Ionotropic glutamate receptor	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Glutamate-gated Ion Channel (GIC) family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	MemProtMD	Annotated as membrane protein by MemProtMD

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.