4KCC | pdb_00004kcc

Crystal Structure of the NMDA Receptor GluN1 Ligand Binding Domain Apo State

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	d4kcca_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	N-methyl-D-aspartate receptor subunit 1	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ], brown rat,rat,rats (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	LysR_substrate	e4kccA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Glutamate receptor ionotropic, NMDA 1	transmitter-gated monoatomic ion channel activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmitter-gated monoatomic ion channel activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity amyloid-beta binding binding peptide binding cation binding organic acid binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding protein-containing complex binding protein binding calmodulin binding calcium ion binding metal ion binding signaling receptor binding voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity transmembrane signaling receptor activity NMDA glutamate receptor activity glutamate receptor activity carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity phosphatase binding enzyme binding calcium channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity ligand-gated sodium channel activity sodium channel activity sodium ion transmembrane transporter activity ligand-gated monoatomic cation channel activity glutamate receptor binding ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ligand-gated calcium channel activity glutamate-gated calcium ion channel activity voltage-gated monoatomic cation channel activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential glutamate binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process 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 positive regulation of signaling behavior learning or memory cognition memory reproductive process male mating behavior multicellular organismal reproductive process reproductive behavior mating behavior transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse localization within membrane protein localization to membrane macromolecule localization protein localization to postsynapse intracellular protein localization protein localization to cell junction startle response neuromuscular process response to external stimulus suckling behavior feeding behavior inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis response to morphine response to isoquinoline alkaloid response to chemical response to nitrogen compound response to alkaloid regulation of localization regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport regulation of calcium ion transport into cytosol regulation of monoatomic ion transmembrane transport regulation of calcium ion transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration positive regulation of calcium ion transport into cytosol regulation of transmembrane transport positive regulation of transport regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transport into cytosol regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development regulation of synapse structure or activity regulation of synapse assembly synapse organization cellular component organization or biogenesis system development developmental process nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly regulation of respiratory gaseous exchange respiratory gaseous exchange by respiratory system cellular homeostasis neuron cellular homeostasis protein-containing complex organization protein-containing complex assembly regulation of neuron projection development axonogenesis cellular developmental process regulation of developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of axonogenesis cell differentiation regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic dendritic spine maintenance positive regulation of cellular component organization cellular component maintenance regulation of dendritic spine maintenance positive regulation of dendritic spine maintenance positive regulation of cell projection organization dendritic spine organization postsynapse organization regulation of postsynapse organization neuron projection organization cellular response to metal ion cellular response to chemical stimulus response to metal ion cellular response to manganese ion response to manganese ion sodium ion transmembrane transport sodium ion transport response to antibiotic response to fungicide response to toxic substance pons development head development hindbrain maturation central nervous system maturation pons maturation animal organ development brain development developmental maturation central nervous system development anatomical structure maturation metencephalon development hindbrain development biological process involved in intraspecies interaction between organisms social behavior ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway reactive oxygen species biosynthetic process regulation of biosynthetic process positive regulation of reactive oxygen species biosynthetic process reactive oxygen species metabolic process regulation of reactive oxygen species biosynthetic process positive regulation of reactive oxygen species metabolic process positive regulation of metabolic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of metabolic process regulation of reactive oxygen species metabolic process dendrite development regulation of dendrite morphogenesis dendrite morphogenesis regulation of dendrite development learning associative learning response to amine response to amphetamine sensory perception sensory perception of pain conditioned taste aversion response to calcium ion olfactory behavior chemosensory behavior olfactory learning positive regulation of locomotion regulation of cell motility glial cell migration regulation of Schwann cell migration regulation of glial cell migration positive regulation of cell migration positive regulation of Schwann cell migration gliogenesis positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion Schwann cell migration positive regulation of glial cell migration regulation of locomotion positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death intracellular calcium ion homeostasis intracellular monoatomic cation homeostasis intracellular chemical homeostasis intracellular monoatomic ion homeostasis regulation of response to external stimulus negative regulation of response to stimulus negative regulation of biological process prepulse inhibition negative regulation of response to external stimulus regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of long-term neuronal synaptic plasticity forebrain development pallium development cerebral cortex development telencephalon development response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription protein heterotetramerization protein complex oligomerization protein tetramerization protein heterooligomerization adult locomotory behavior adult behavior locomotory behavior neuron apoptotic process regulation of neuron apoptotic process response to acid chemical response to glycine response to oxygen-containing compound response to amino acid response to light stimulus visual learning visual behavior response to radiation negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process cellular response to xenobiotic stimulus propylene metabolic process xenobiotic metabolic process response to xenobiotic stimulus hydrocarbon metabolic process olefinic compound metabolic process olefin metabolic process response to alcohol response to ethanol long-term memory rhythmic process cellular response to acid chemical cellular response to nitrogen compound cellular response to amino acid stimulus cellular response to glycine cellular response to oxygen-containing compound response to glycoside	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 parallel fiber to Purkinje cell synapse excitatory synapse protein-containing complex neurotransmitter receptor complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex receptor complex neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle secretory vesicle cytoplasm vesicle exocytic vesicle transmembrane transporter complex transporter complex monoatomic ion channel complex NMDA selective glutamate receptor complex ionotropic glutamate receptor complex cell surface organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane presynaptic active zone membrane presynaptic membrane presynaptic active zone hippocampal mossy fiber to CA3 synapse cell leading edge leading edge membrane neuron projection membrane dendrite membrane cell projection membrane dendritic branch synaptic cleft extracellular region basal part of cell basal plasma membrane basolateral plasma membrane glutamatergic synapse cell body neuronal cell body transport vesicle membrane bounding membrane of organelle vesicle membrane synaptic vesicle membrane exocytic vesicle membrane cytoplasmic vesicle membrane axon axon terminus distal axon terminal bouton neuron projection terminus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A	IPR001828	Receptor, ligand binding region	Domain
A	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A	IPR049873	Glutamate [NMDA] receptor subunit 1-like, N-terminal LIVBP-like domain	Domain
A	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A	IPR015683	Ionotropic glutamate receptor	Family
A	IPR049872	Glutamate [NMDA] receptor subunit 1-like, ligand-binding domain	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.