5B3J | pdb_00005b3j

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil

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
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth L]	d5b3jl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth L]	d5b3jl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d5b3jf2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d5b3jf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth H]	d5b3jh_	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 E]	d5b3je_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	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)
H [auth L]	Glutaminase	e5b3jL1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glutaminase	ECOD (v294.1)
F	Glutaminase	e5b3jF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glutaminase	ECOD (v294.1)
G [auth H]	Glutaminase	e5b3jH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glutaminase	ECOD (v294.1)
D [auth E]	Glutaminase	e5b3jE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glutaminase	ECOD (v294.1)
E [auth D]	Glutaminase	e5b3jD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glutaminase	ECOD (v294.1)
C	Glutaminase	e5b3jC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glutaminase	ECOD (v294.1)
B	MMS1_N	e5b3jB1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (v294.1)
A	MMS1_N	e5b3jA1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth D]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	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)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F, H [auth L]	Light Chain	IGKV19	Kappa	glutamate receptor ionotropic, nmda 2b	SAbDab (2026-03-27)
D [auth E], G [auth H]	Heavy Chain	IGHV5	-	glutamate receptor ionotropic, nmda 2b	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, E [auth D]	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, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, H [auth L]	Fab, light chain	-	-	-
D [auth E], G [auth H]	Fab, heavy chain	-	-	-
C, E [auth D]	Glutamate receptor ionotropic, NMDA 2B	protein binding binding interleukin-1 receptor binding signaling receptor binding cytokine receptor binding growth factor receptor binding cation binding organic acid binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding protein binding binding interleukin-1 receptor binding signaling receptor binding cytokine receptor binding growth factor receptor binding cation binding organic acid binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding gated channel activity monoatomic ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity extracellularly glutamate-gated ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity protein-containing complex binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding D2 dopamine receptor binding G protein-coupled receptor binding dopamine receptor binding cell adhesion molecule binding scaffold protein binding heterocyclic compound binding beta-catenin binding transmitter-gated monoatomic ion channel activity molecular transducer activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity transmembrane signaling receptor activity NMDA glutamate receptor activity glutamate receptor activity signaling receptor activity carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity transmitter-gated channel activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity calcium channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity 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 ionotropic glutamate receptor binding protein serine/threonine kinase binding transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential transition metal ion binding zinc ion binding metal ion binding 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 response to chemical response to methylmercury response to antibiotic 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 behavior learning or memory cognition memory response to toxic substance response to stress multicellular organismal response to stress response to pain behavioral response to pain regulation of cAMP/PKA signal transduction intracellular signal transduction cAMP/PKA signal transduction regulation of intracellular signal transduction intracellular signaling cassette startle response neuromuscular process suckling behavior feeding behavior response to growth hormone response to hormone response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound localization cellular localization receptor clustering macromolecule localization intracellular protein localization localization within membrane protein localization to membrane response to auditory stimulus auditory behavior response to mechanical stimulus response to abiotic stimulus mechanosensory behavior response to metal ion response to manganese ion detection of external stimulus detection of mechanical stimulus involved in sensory perception of pain sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus detection of stimulus involved in sensory perception synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic transport monoatomic ion transport monoatomic cation transport establishment of localization response to peptide response to cytokine cellular response to metal ion cellular response to chemical stimulus cellular response to manganese ion response to lead ion cellular response to endogenous stimulus cellular response to growth factor stimulus response to growth factor response to fungicide small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction ARF protein signal transduction regulation of ARF protein signal transduction ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway negative regulation of signaling negative regulation of biological process negative regulation of synaptic transmission negative regulation of cell communication negative regulation of cellular process regulation of synaptic plasticity long-term synaptic depression regulation of long-term synaptic depression learning associative learning response to amine response to amphetamine calcium ion transport metal ion transport regulation of localization nitrogen compound transport regulation of glutamate secretion positive regulation of secretion by cell positive regulation of amine transport secretion by cell regulation of secretion by cell positive regulation of secretion regulation of amino acid transport glutamate secretion organic anion transport carboxylic acid transport secretion regulation of transport positive regulation of glutamate secretion export from cell regulation of secretion positive regulation of organic acid transport organic acid transport amino acid transport amine transport acidic amino acid transport positive regulation of transport positive regulation of amino acid transport regulation of organic acid transport dicarboxylic acid transport regulation of amine transport response to carbohydrate response to ketone response to lipid response to alcohol cellular response to forskolin cellular response to oxygen-containing compound cellular response to alcohol response to forskolin cellular response to lipid cellular response to ketone cellular response to nitrogen compound cellular response to dsRNA response to dsRNA 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 regulation of MAPK cascade MAPK cascade 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 fear response developmental process multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development response to electrical stimulus regulation of neuronal synaptic plasticity regulation of long-term neuronal synaptic plasticity head development forebrain development animal organ development brain development nervous system development pallium development cerebral cortex development central nervous system development telencephalon development system development cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid response to decreased oxygen levels response to hypoxia response to oxygen levels monoatomic cation transmembrane transport transmembrane transport monoatomic ion transmembrane transport regulation of cellular component organization dendritic spine maintenance cell projection organization cellular component maintenance regulation of dendritic spine maintenance cellular component organization regulation of synapse structure or activity cellular component organization or biogenesis synapse organization negative regulation of cell projection organization negative regulation of dendritic spine maintenance plasma membrane bounded cell projection organization dendritic spine organization postsynapse organization negative regulation of cellular component organization regulation of cell projection organization regulation of postsynapse organization regulation of synapse organization cell junction organization neuron projection organization regulation of plasma membrane bounded cell projection organization response to curcumin cellular response to ether response to ether cellular response to curcumin response to hydrogen sulfide cellular response to nutrient levels response to nutrient levels cellular response to stress response to starvation cellular response to starvation cellular response to magnesium starvation protein-containing complex organization protein heterotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein heterooligomerization hippocampus development limbic system development action potential nonassociative learning sensitization regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport response to ethanol long-term memory sensory organ development rhythmic process calcium ion transmembrane import into cytosol calcium ion transmembrane transport behavioral defense response behavioral fear response defense response cellular response to mineralocorticoid stimulus response to corticosterone response to mineralocorticoid response to steroid hormone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosterone stimulus cellular response to corticosteroid stimulus response to corticosteroid response to nicotine long-term synaptic potentiation response to glycoside cellular developmental process cell development generation of neurons neurogenesis neuron differentiation cell differentiation neuron development response to cocaine response to alkaloid 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 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 ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex cell surface lytic vacuole vacuole lysosome 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 endosome late endosome apical dendrite dendritic branch intracellular membraneless organelle Z disc sarcomere I band membraneless organelle contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex synaptic cleft extracellular region glutamatergic synapse cytoskeleton cell body neuronal cell body postsynaptic density, intracellular component postsynaptic specialization, intracellular component axon axon terminus distal axon terminal bouton neuron projection terminus
A, B	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 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 ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, E [auth D]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluN1a/GluN2B NMDA receptor, apo-form crystal structure

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.