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- PDB-9gie: NMDA bound to compound 315 -

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Basic information

Entry
Database: PDB / ID: 9gie
TitleNMDA bound to compound 315
ComponentsGlutamate receptor ionotropic, NMDA 1
KeywordsTRANSPORT PROTEIN / ion transport ligand gated ion channel
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / Neurexins and neuroligins / ligand-gated sodium channel activity / glutamate binding / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of calcium ion transport into cytosol / Long-term potentiation / monoatomic cation transport / excitatory synapse / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / excitatory postsynaptic potential / regulation of membrane potential / postsynaptic density membrane / brain development / calcium ion transmembrane transport / visual learning / regulation of synaptic plasticity / terminal bouton / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / dendritic spine / postsynaptic membrane / calmodulin binding / neuron projection / postsynaptic density / dendrite / synapse / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm
Similarity search - Function
: / : / 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. ...: / : / 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
: / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 19, 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 ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5514
Polymers66,8442
Non-polymers7072
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-9 kcal/mol
Surface area23610 Å2
Unit cell
Length a, b, c (Å)72.448, 78.868, 91.984
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33422.141 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-A1ILS / (2~{R})-2-azanyl-3-[[4-(2-ethylphenyl)-2,3-dihydro-1~{H}-indol-2-yl]carbonylamino]propanoic acid


Mass: 353.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% PEG 3350 and 0.1 M hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.36→91.98 Å / Num. obs: 22308 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 1 / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.8
Reflection shellResolution: 2.36→2.4 Å / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1079 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→59.945 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.229 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.282
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1115 5.009 %RANDOM
Rwork0.1941 21143 --
all0.197 ---
obs-22258 99.865 %-
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: 50.194 Å2
Baniso -1Baniso -2Baniso -3
1-0.734 Å2-0 Å20 Å2
2---2.862 Å2-0 Å2
3---2.128 Å2
Refinement stepCycle: LAST / Resolution: 2.36→59.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 52 55 4298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163970
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.8345888
X-RAY DIFFRACTIONr_angle_other_deg0.5031.7689166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.659516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16210711
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.65910184
X-RAY DIFFRACTIONr_chiral_restr0.070.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined0.1810.2700
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.23486
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22099
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22337
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.212
X-RAY DIFFRACTIONr_nbd_other0.170.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.24
X-RAY DIFFRACTIONr_mcbond_it4.5775.0212162
X-RAY DIFFRACTIONr_mcbond_other4.5765.0212162
X-RAY DIFFRACTIONr_mcangle_it6.8389.0282692
X-RAY DIFFRACTIONr_mcangle_other6.8379.0282693
X-RAY DIFFRACTIONr_scbond_it4.7775.2172180
X-RAY DIFFRACTIONr_scbond_other4.7765.2172181
X-RAY DIFFRACTIONr_scangle_it7.2859.4913196
X-RAY DIFFRACTIONr_scangle_other7.2849.4913197
X-RAY DIFFRACTIONr_lrange_it10.68459.33616839
X-RAY DIFFRACTIONr_lrange_other10.68759.35516822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.36-2.4210.335800.27615310.27916170.9050.9499.62890.267
2.421-2.4870.31710.27115150.27315870.9290.94899.9370.255
2.487-2.5590.379810.2414290.24615110.8970.9699.93380.222
2.559-2.6380.331660.2414350.24415010.9370.9611000.218
2.638-2.7240.308760.22413720.22914480.9410.9641000.201
2.724-2.820.277860.21313250.21614130.9490.96999.85850.184
2.82-2.9260.342690.20912710.21613410.9230.9799.92540.186
2.926-3.0450.267550.20812560.21113120.950.96999.92380.187
3.045-3.180.292550.212100.20412660.9280.97299.9210.186
3.18-3.3350.272510.19911450.20211970.9520.97299.91650.185
3.335-3.5150.306630.20710770.21211400.9340.9731000.199
3.515-3.7270.201460.17410480.17610960.9720.9899.81750.169
3.727-3.9830.221640.1539620.15710280.9720.98699.80550.154
3.983-4.3010.212510.1489140.1519680.9660.98699.69010.154
4.301-4.7090.184480.1478440.1498950.9820.98699.66480.16
4.709-5.2610.253550.1657600.178160.9590.98399.87750.181
5.261-6.0670.24340.2056960.2067310.9660.97599.86320.216
6.067-7.4110.377210.2095890.2156100.9280.971000.226
7.411-10.4020.2280.1844720.1855010.9820.97899.80040.217
10.402-59.9450.295150.2522920.2543100.9260.95599.03230.3

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