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- PDB-9gj1: NMDA bound to compound 339 -

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Basic information

Entry
Database: PDB / ID: 9gj1
TitleNMDA bound to compound 339
Components
  • Glutamate receptor
  • Isoform 1 of Glutamate receptor ionotropic, NMDA 1
KeywordsTRANSPORT PROTEIN / ion transport ligand gated ion channel
Function / homology
Function and homology information


neurotransmitter receptor complex / excitatory chemical synaptic transmission / directional locomotion / serotonin metabolic process / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / regulation of monoatomic cation transmembrane transport ...neurotransmitter receptor complex / excitatory chemical synaptic transmission / directional locomotion / serotonin metabolic process / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / transmitter-gated monoatomic ion channel activity / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / startle response / Negative regulation of NMDA receptor-mediated neuronal transmission / dopamine metabolic process / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / monoatomic cation transport / Long-term potentiation / positive regulation of excitatory postsynaptic potential / excitatory synapse / ligand-gated monoatomic ion channel activity / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / sensory perception of pain / EPHB-mediated forward signaling / response to amphetamine / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / neurogenesis / long-term synaptic potentiation / synaptic membrane / protein catabolic process / postsynaptic density membrane / visual learning / terminal bouton / brain development / negative regulation of protein catabolic process / regulation of synaptic plasticity / response to wounding / calcium ion transmembrane transport / memory / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / RAF/MAP kinase cascade / chemical synaptic transmission / response to ethanol / postsynaptic membrane / dendritic spine / calmodulin binding / postsynaptic density / neuron projection / positive regulation of apoptotic process / response to xenobiotic stimulus / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
: / GLUTAMIC ACID / Glutamate receptor / Glutamate receptor / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsCarr, K.H. / Ascic, E. / Leonard, P.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Advancements in NMDA Receptor-Targeted Antidepressants: From d-Cycloserine Discovery to Preclinical Efficacy of Lu AF90103.
Authors: Ascic, E. / Marigo, M. / David, L. / Frisch Herrik, K. / Grupe, M. / Hougaard, C. / Mork, A. / Jones, C.R. / Badolo, L. / Frederiksen, K. / Boonen, H.C.M. / Jensen, H.S. / Kilburn, J.P.
History
DepositionAug 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor
B: Isoform 1 of Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7235
Polymers65,2042
Non-polymers5193
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-8 kcal/mol
Surface area24140 Å2
Unit cell
Length a, b, c (Å)54.037, 88.143, 119.761
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Glutamate receptor


Mass: 31939.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a, HJG63_005955 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: G3V9C5, UniProt: A0A7J8EZV6
#2: Protein Isoform 1 of Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33264.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3) / References: UniProt: Q05586

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Non-polymers , 4 types, 361 molecules

#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-A1IME / (2~{R})-2-azanyl-3-[(7-methylthieno[3,2-b]pyridin-2-yl)carbonylamino]propanoic acid


Mass: 279.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13N3O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.62→59.85 Å / Num. obs: 71100 / % possible obs: 96.9 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Net I/σ(I): 13.2
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4136 / CC1/2: 0.487 / Rpim(I) all: 0.582 / % possible all: 78.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→59.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.553 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 3451 4.882 %RANDOM
Rwork0.2005 67241 --
all0.202 ---
obs-70692 96.233 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.677 Å2-0 Å20 Å2
2--0.429 Å20 Å2
3---0.248 Å2
Refinement stepCycle: LAST / Resolution: 1.62→59.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4274 0 35 358 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124439
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164071
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.8186030
X-RAY DIFFRACTIONr_angle_other_deg0.5871.7559401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.5876.36422
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg7.21951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70310730
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.02310194
X-RAY DIFFRACTIONr_chiral_restr0.0860.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
X-RAY DIFFRACTIONr_nbd_refined0.2180.2837
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23762
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22240
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2312
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.210
X-RAY DIFFRACTIONr_nbd_other0.1870.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.28
X-RAY DIFFRACTIONr_mcbond_it2.5592.4332229
X-RAY DIFFRACTIONr_mcbond_other2.5592.4332229
X-RAY DIFFRACTIONr_mcangle_it3.6364.3632783
X-RAY DIFFRACTIONr_mcangle_other3.6364.3622784
X-RAY DIFFRACTIONr_scbond_it3.162.6592210
X-RAY DIFFRACTIONr_scbond_other3.1612.662208
X-RAY DIFFRACTIONr_scangle_it4.8074.763243
X-RAY DIFFRACTIONr_scangle_other4.8074.7593244
X-RAY DIFFRACTIONr_lrange_it6.71729.37818709
X-RAY DIFFRACTIONr_lrange_other6.64929.24118404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.6620.3872130.3843828X-RAY DIFFRACTION75.1115
1.662-1.7080.3662390.3674270X-RAY DIFFRACTION86.6116
1.708-1.7570.3562140.3254526X-RAY DIFFRACTION92.8138
1.757-1.8110.2892290.294551X-RAY DIFFRACTION96.3127
1.811-1.8710.2912320.2524454X-RAY DIFFRACTION98.1567
1.871-1.9360.2872220.2334398X-RAY DIFFRACTION99.4832
1.936-2.0090.2422280.2074242X-RAY DIFFRACTION99.6656
2.009-2.0910.2482140.1984098X-RAY DIFFRACTION99.8148
2.091-2.1840.2092000.1893927X-RAY DIFFRACTION99.7824
2.184-2.2910.2291750.1883804X-RAY DIFFRACTION99.5746
2.291-2.4140.1941760.1763577X-RAY DIFFRACTION99.8935
2.414-2.560.2331810.1813434X-RAY DIFFRACTION99.7792
2.56-2.7370.2072030.1743178X-RAY DIFFRACTION99.9113
2.737-2.9560.221250.183021X-RAY DIFFRACTION99.9047
2.956-3.2370.2191450.1712799X-RAY DIFFRACTION100
3.237-3.6180.1981410.1732511X-RAY DIFFRACTION100
3.618-4.1750.191290.1662235X-RAY DIFFRACTION100
4.175-5.1070.182800.1651940X-RAY DIFFRACTION100
5.107-7.1960.218550.231535X-RAY DIFFRACTION99.9371
7.196-59.850.255500.217913X-RAY DIFFRACTION100

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