3QXM

Crystal Structure of Human GluK2 Ligand-Binding Core in Complex with Novel Marine-Derived Toxins, Neodysiherbaine A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Phosphate binding protein-like	8099155	4000229	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Type 2 solute binding protein-like	8099156	3000083	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Lig_chan_1	e3qxmB1	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	Lig_chan_2	e3qxmB2	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)
A	Lig_chan_1	e3qxmA2	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	Lig_chan_2	e3qxmA3	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)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
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, 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 2	protein binding binding PDZ domain binding protein domain specific binding 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 protein binding binding PDZ domain binding protein domain specific binding 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 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 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 organic acid transmembrane transporter activity organic anion transmembrane transporter activity ubiquitin-like protein conjugating enzyme binding enzyme binding ubiquitin conjugating enzyme binding SNARE binding excitatory extracellular ligand-gated monoatomic ion channel activity extracellularly glutamate-gated ion channel 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 ubiquitin protein ligase binding ubiquitin-like protein ligase binding 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 identical protein 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 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 glutamate receptor signaling pathway 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 negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of cellular process regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of short-term neuronal synaptic plasticity action potential transmission of nerve impulse neuronal action potential regulation of long-term neuronal synaptic plasticity negative regulation of signaling synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic negative regulation of synaptic transmission negative regulation of cell communication negative regulation of synaptic transmission, glutamatergic inhibitory postsynaptic potential behavioral defense response behavior fear response behavioral fear response defense response response to stress multicellular organismal response to stress 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	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 mossy fiber rosette presynaptic membrane glutamatergic synapse neuron projection cytoplasm intracellular anatomical structure cytoplasmic region plasma membrane bounded cell projection cytoplasm dendrite cytoplasm dendrite dendritic tree cytoplasm hippocampal mossy fiber to CA3 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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13002	intellectual disability, autosomal recessive 6 bipolar disorder intellectual disability schizophrenia hypoactive sexual desire disorder large cell medulloblastoma lung carcinoma malignant mesothelioma Manic Disorder astrocytic tumor autism subependymal giant cell astrocytoma epilepsy substance dependence Lennox-Gastaut syndrome intellectual disability, autosomal recessive 6 bipolar disorder intellectual disability schizophrenia hypoactive sexual desire disorder large cell medulloblastoma lung carcinoma malignant mesothelioma Manic Disorder astrocytic tumor autism subependymal giant cell astrocytoma epilepsy substance dependence Lennox-Gastaut syndrome malignant ependymoma medulloblastoma oligodendroglioma attention deficit hyperactivity disorder, inattentive type osteosarcoma substance abuse glioblastoma lung cancer malignant glioma atypical teratoid rhabdoid tumor ovarian cancer drug dependence Sjogren syndrome endogenous depression epilepsy with generalized tonic-clonic seizures substance-related disorder

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.