6IRH | pdb_00006irh

Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class III

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth B]		e6irhB1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PTE	F:	ECOD (20:10:01)
B [auth D]		e6irhD1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PTE	F:	ECOD (20:10:01)
C [auth A]		e6irhA1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PTE	F:	ECOD (20:10:01)
A [auth C]		e6irhC1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PTE	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth B]	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
B [auth D], D [auth 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
A [auth C], C [auth A]	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A [auth C], C [auth A]	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 [auth C], C [auth A]	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
B [auth D], D [auth B]	Glutamate receptor ionotropic, NMDA 2A	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel activity transmembrane transporter activity amyloid-beta binding binding peptide binding monoatomic cation transmembrane transporter activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate-gated calcium ion channel activity monoatomic cation channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction 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 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 catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process glutamate receptor signaling pathway behavior learning or memory cognition memory amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process dopamine metabolic process catechol-containing compound metabolic process biogenic amine metabolic process 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 regulation of neuronal synaptic plasticity regulation of synaptic plasticity response to stress response to wounding negative regulation of biological process negative regulation of protein catabolic process regulation of primary metabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of metabolic process regulation of protein catabolic process neurogenesis cellular developmental process cell differentiation synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic regulation of localization regulation of transport regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport response to light stimulus learning visual learning visual behavior associative learning response to radiation response to abiotic stimulus serotonin metabolic process indole-containing compound metabolic process response to alcohol response to oxygen-containing compound response to ethanol sodium ion transmembrane transport sodium ion transport sleep directional locomotion locomotion calcium ion transmembrane import into cytosol ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway response to amine response to nitrogen compound response to amphetamine excitatory chemical synaptic transmission sensory perception sensory perception of pain 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 presynapse presynaptic membrane glutamatergic synapse 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 cytoplasmic vesicle synaptic vesicle secretory vesicle cytoplasm vesicle exocytic vesicle protein-containing complex plasma membrane protein complex membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex cell surface organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cytoplasmic vesicle membrane vesicle membrane
A [auth C], C [auth A]	Glutamate receptor ionotropic, NMDA 1	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel 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 monoatomic cation transmembrane transporter activity monoatomic cation channel activity glycine-gated cation channel activity ligand-gated monoatomic cation channel activity calcium ion binding metal ion binding ligand-gated sodium channel activity sodium channel activity sodium ion transmembrane transporter activity metal ion transmembrane transporter activity ligand-gated calcium channel activity calcium channel activity glutamate-gated calcium ion channel activity calcium ion transmembrane transporter activity glutamate binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication 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 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 regulation of neuronal synaptic plasticity regulation of synaptic plasticity inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis regulation of localization regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport cellular localization 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 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 positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of 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 biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis protein heterooligomerization synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic response to acid chemical response to glycine response to chemical response to oxygen-containing compound response to nitrogen compound response to amino acid response to light stimulus learning learning or memory visual learning visual behavior cognition associative learning behavior response to radiation response to abiotic stimulus cellular response to xenobiotic stimulus propylene metabolic process xenobiotic metabolic process response to xenobiotic stimulus hydrocarbon metabolic process cellular response to chemical stimulus olefinic compound metabolic process olefin metabolic process response to alcohol response to ethanol sodium ion transmembrane transport sodium ion transport ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway reactive oxygen species 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 regulation of reactive oxygen species metabolic process excitatory chemical synaptic transmission	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 synaptic cleft extracellular region somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm protein-containing complex neurotransmitter receptor complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex receptor complex neuron spine dendritic spine membrane-bounded organelle transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle secretory vesicle vesicle exocytic vesicle axon axon terminus distal axon terminal bouton neuron projection terminus transporter complex NMDA selective glutamate receptor complex ionotropic glutamate receptor complex transmembrane transporter complex monoatomic ion channel complex cell surface organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane excitatory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth B]	IPR018884	Glutamate [NMDA] receptor, epsilon subunit, C-terminal	Domain
B [auth D], D [auth B]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
B [auth D], D [auth B]	IPR001508	Ionotropic glutamate receptor, metazoa	Family
B [auth D], D [auth B]	IPR001828	Receptor, ligand binding region	Domain
B [auth D], D [auth B]	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
B [auth D], D [auth B]	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
B [auth D], D [auth B]	IPR015683	Ionotropic glutamate receptor	Family
A [auth C], C [auth A]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A [auth C], C [auth A]	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A [auth C], C [auth A]	IPR001828	Receptor, ligand binding region	Domain
A [auth C], C [auth A]	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A [auth C], C [auth A]	IPR049873	Glutamate [NMDA] receptor subunit 1-like, N-terminal LIVBP-like domain	Domain
A [auth C], C [auth A]	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A [auth C], C [auth A]	IPR015683	Ionotropic glutamate receptor	Family
A [auth C], C [auth A]	IPR049872	Glutamate [NMDA] receptor subunit 1-like, ligand-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D], D [auth B]	Pharos: Q12879	Landau-Kleffner syndrome epilepsy rolandic epilepsy melanoma autism colorectal cancer morphine dependence schizophrenia substance withdrawal syndrome bipolar disorder speech disorder Language Development Disorders depressive disorder oligodendroglioma Parkinson disease Landau-Kleffner syndrome epilepsy rolandic epilepsy melanoma autism colorectal cancer morphine dependence schizophrenia substance withdrawal syndrome bipolar disorder speech disorder Language Development Disorders depressive disorder oligodendroglioma Parkinson disease pilocytic astrocytoma psoriasis subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor large cell medulloblastoma lung carcinoma medulloblastoma continuous spikes and waves during sleep opiate dependence postencephalitic Parkinson disease glioblastoma astrocytic tumor auditory perceptual disorders Lennox-Gastaut syndrome autism spectrum disorder malignant ependymoma colorectal carcinoma cutaneous melanoma neurodegenerative disease ovarian cancer Pick disease primitive neuroectodermal tumor hepatitis B virus infection intellectual disability attention deficit hyperactivity disorder, inattentive type toxic encephalopathy malignant glioma
A [auth C], C [auth A]	Pharos: Q05586	intellectual disability, autosomal dominant 8 Pain cocaine dependence intellectual disability trigeminal neuralgia cocaine abuse schizoaffective disorder lung adenocarcinoma neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive atypical teratoid rhabdoid tumor postencephalitic Parkinson disease glioblastoma schizophreniform disorder Sjogren syndrome large cell medulloblastoma intellectual disability, autosomal dominant 8 Pain cocaine dependence intellectual disability trigeminal neuralgia cocaine abuse schizoaffective disorder lung adenocarcinoma neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive atypical teratoid rhabdoid tumor postencephalitic Parkinson disease glioblastoma schizophreniform disorder Sjogren syndrome large cell medulloblastoma malignant ependymoma medulloblastoma oligodendroglioma bipolar disorder Pick disease primitive neuroectodermal tumor subependymal giant cell astrocytoma malignant glioma osteosarcoma astrocytic tumor Parkinson disease pilocytic astrocytoma

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth C], B [auth D], C [auth A], D [auth B]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth C], B [auth D], C [auth A], D [auth B]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth C], B [auth D], C [auth A], D [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 7.8

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.