5UN1 | pdb_00005un1

Crystal structure of GluN1/GluN2B delta-ATD NMDA receptor

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
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)
A [auth G]	NADHdh	e5un1G1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: NADHdh	ECOD (v294.1)
B [auth A]	Gp34_trimer, Gp34_2nd, PF31249	e5un1A3	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Gp34_trimer, Gp34_2nd, PF31249	ECOD (v294.1)
B [auth A]	Ald_deCOase	e5un1A1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Ald_deCOase	ECOD (v294.1)
E	BacA	e5un1E1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: tetra-helical, lambda repressor-like	F: BacA	ECOD (v294.1)
G [auth C]	BacA	e5un1C1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: tetra-helical, lambda repressor-like	F: BacA	ECOD (v294.1)
C [auth B]	Ald_deCOase	e5un1B1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Ald_deCOase	ECOD (v294.1)
H [auth D]	Glyco_hydro_70	e5un1D3	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Glyco_hydro_70	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth G]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B [auth A]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
E	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
G [auth C]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
C [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
D [auth H]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
F	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
H [auth D]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G], B [auth A], E, G [auth C]	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A [auth G], B [auth A], E, G [auth C]	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
C [auth B], D [auth H], F, H [auth D]	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
C [auth B], D [auth H], F, H [auth D]	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 [auth G], B [auth A], E, G [auth C]	N-methyl-D-aspartate receptor subunit NR1-3a	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 monoatomic cation transmembrane transporter activity ligand-gated sodium channel activity sodium channel activity sodium ion transmembrane transporter activity monoatomic cation channel activity metal ion transmembrane transporter activity ligand-gated monoatomic cation channel activity ligand-gated calcium channel activity calcium channel activity glutamate-gated calcium ion channel activity calcium ion transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	transport monoatomic ion transmembrane transport sodium ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport sodium ion transport calcium ion transport calcium ion transmembrane transport transport monoatomic ion transmembrane transport sodium ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport sodium ion transport calcium ion transport calcium ion transmembrane transport response to stimulus response to metal ion response to chemical response to zinc ion biological regulation regulation of biological quality regulation of membrane potential trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission cell communication regulation of synaptic plasticity regulation of signaling regulation of cellular process modulation of chemical synaptic transmission regulation of trans-synaptic signaling regulation of cell communication cellular response to stimulus ligand-gated ion channel signaling pathway cell surface receptor signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway signal transduction	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 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 projection neuron projection plasma membrane bounded cell projection
C [auth B], D [auth H], F, H [auth D]	Ionotropic glutamate receptor subunit NR2B	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 transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential 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 cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process signaling chemical synaptic transmission, postsynaptic cell communication synaptic signaling signal transduction response to stimulus response to metal ion response to chemical response to zinc ion cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process signaling chemical synaptic transmission, postsynaptic cell communication synaptic signaling signal transduction regulation of biological quality trans-synaptic signaling regulation of biological process cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission anterograde trans-synaptic signaling cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of cell communication modulation of chemical synaptic transmission positive regulation of biological process long-term synaptic potentiation positive regulation of cellular process regulation of synaptic plasticity regulation of signaling positive regulation of synaptic transmission regulation of trans-synaptic signaling regulation of cell communication positive regulation of signaling synaptic transmission, glutamatergic response to magnesium ion	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 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 membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle late endosome cytoplasm vesicle lytic vacuole vacuole lysosome

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth G], B [auth A], C [auth B], D [auth H], E A [auth G], B [auth A], C [auth B], D [auth H], E, F, G [auth C], H [auth D]	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 [auth G], B [auth A], C [auth B], D [auth H], E A [auth G], B [auth A], C [auth B], D [auth H], E, F, G [auth C], H [auth D]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth G], B [auth A], C [auth B], D [auth H], E A [auth G], B [auth A], C [auth B], D [auth H], E, F, G [auth C], H [auth D]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluN1a/GluN2B NMDA receptor lacking N-terminal domain (ΔATD)

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.