5TPW

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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 [auth H]	d5tpwh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d5tpwl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d5tpwl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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)
A	ANF_receptor_3rd	e5tpwA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: ANF_receptor_3rd	ECOD (1.6)
A	ANF_receptor_2nd	e5tpwA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: ANF_receptor_2nd	ECOD (1.6)
B	ANF_receptor_3rd	e5tpwB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: ANF_receptor_3rd	ECOD (1.6)
B	ANF_receptor_2nd	e5tpwB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: ANF_receptor_2nd	ECOD (1.6)
C [auth H]	V-set_8	e5tpwH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e5tpwH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth L]	C1-set_4	e5tpwL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth L]	V-set	e5tpwL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV9	-	nmda glutamate receptor subunit \| glutamate receptor ionotropic, nmda 2a	SAbDab (2024-10-25)
D [auth L]	Light Chain	IGKV5	Kappa	nmda glutamate receptor subunit \| glutamate receptor ionotropic, nmda 2a	SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	NMDA glutamate receptor subunit	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 inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor 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 inorganic molecular entity transmembrane transporter activity inorganic cation 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 organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to metal ion response to chemical response to zinc ion	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane 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
B	Glutamate receptor ionotropic, NMDA 2A	protein-containing complex binding binding protein tyrosine kinase binding protein binding kinase binding enzyme binding protein kinase binding signaling receptor binding cell adhesion molecule binding scaffold protein binding calcium-dependent protein binding transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity protein-containing complex binding binding protein tyrosine kinase binding protein binding kinase binding enzyme binding protein kinase binding signaling receptor binding cell adhesion molecule binding scaffold protein binding calcium-dependent protein binding 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 inorganic molecular entity transmembrane transporter activity inorganic cation 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 organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity calcium channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity ATPase binding glutamate receptor binding ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ligand-gated calcium channel activity ligand-gated monoatomic cation 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 postsynaptic neurotransmitter receptor activity neurotransmitter receptor 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 organic acid binding anion binding amino acid binding carboxylic acid binding glutamate binding	response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process 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 positive regulation of cell communication positive regulation of signal transduction positive regulation of excitatory postsynaptic potential positive regulation of biological process positive regulation of response to stimulus positive regulation of cellular process positive regulation of signaling response to methylmercury catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to external biotic stimulus response to biotic stimulus glutamate receptor signaling pathway behavior learning or memory cognition memory amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process organic hydroxy compound metabolic process dopamine metabolic process catechol-containing compound metabolic process biogenic amine metabolic process response to environmental enrichment protein localization protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse localization within membrane protein localization to membrane localization cellular macromolecule localization macromolecule localization protein localization to postsynapse protein localization to cell junction startle response neuromuscular process establishment of protein localization nitrogen compound transport neurotransmitter receptor transport transport protein localization to endosome plasma membrane to endosome transport neurotransmitter receptor transport, plasma membrane to endosome establishment of localization vesicle-mediated transport protein-containing complex localization establishment of protein localization to organelle protein transport protein localization to organelle response to stress response to wounding learning conditioned place preference associative learning receptor metabolic process receptor recycling regulation of response to alcohol response to alcohol response to oxygen-containing compound developmental process multicellular organism development spinal cord development central nervous system development anatomical structure development nervous system development system development response to metal ion response to manganese ion 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 signaling receptor activity regulation of transmembrane transporter activity regulation of transporter activity regulation of NMDA receptor activity regulation of monoatomic ion transmembrane transporter activity regulation of transport transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of neurotransmitter receptor activity cellular response to metal ion cellular response to chemical stimulus cellular response to manganese ion cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor response to antibiotic response to fungicide response to toxic substance response to magnesium ion cellular response to magnesium ion response to zinc ion cellular response to zinc ion small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction ARF protein signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of ARF protein signal transduction intracellular signaling cassette directional locomotion locomotion ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway response to amine response to nitrogen compound response to amphetamine monoatomic ion transport monoatomic cation transport calcium ion transport metal ion transport sensory perception sensory perception of pain response to carbohydrate cellular response to nitrogen compound cellular response to dsRNA cellular response to organic cyclic compound response to dsRNA response to organic cyclic compound positive regulation of inhibitory postsynaptic potential positive regulation of nervous system process modulation of inhibitory postsynaptic potential inhibitory postsynaptic potential positive regulation of multicellular organismal process response to calcium ion 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 response to light stimulus response to radiation response to abiotic stimulus multicellular organismal response to stress regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of long-term neuronal synaptic plasticity response to lithium ion head development forebrain development animal organ development brain development pallium development cerebral cortex development telencephalon development cellular component organization cell junction organization dendritic spine organization postsynapse organization plasma membrane bounded cell projection organization cell projection organization neuron projection organization synapse organization cellular component organization or biogenesis cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid monoatomic cation transmembrane transport monoatomic ion transmembrane transport negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process regulation of catabolic process negative regulation of protein catabolic process regulation of primary metabolic process regulation of metabolic process regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process response to hydrogen sulfide regulation of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane regulation of protein localization to membrane establishment of protein localization to membrane regulation of establishment of protein localization positive regulation of protein localization to membrane protein targeting to membrane regulation of cellular localization regulation of protein targeting positive regulation of protein localization positive regulation of protein targeting to membrane hippocampus development limbic system development action potential regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport regulation of monoatomic cation transmembrane transport visual learning visual behavior ammonium ion metabolic process serotonin metabolic process indole-containing compound metabolic process primary amino compound metabolic process response to ethanol response to ammonium ion sleep rhythmic process response to glycine cellular response to glycine cellular response to oxygen-containing compound calcium ion transmembrane import into cytosol inorganic ion transmembrane transport inorganic cation transmembrane transport calcium ion transmembrane transport response to nicotine long-term synaptic potentiation cell development generation of neurons neuron differentiation neuron development response to cocaine response to alkaloid response to lipid cellular response to lipid	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region parallel fiber to Purkinje cell synapse excitatory 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 presynapse 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 cell leading edge leading edge membrane neuron projection membrane dendrite membrane cell projection membrane presynaptic membrane glutamatergic synapse postsynaptic density, intracellular component postsynaptic specialization, intracellular component intracellular non-membrane-bounded organelle non-membrane-bounded organelle axon axon terminus distal axon terminal bouton neuron projection terminus
C [auth H]	FAB, HEAVY CHAIN	-	-	-
D [auth L]	FAB, LIGHT CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.