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- PDB-9gif: NMDA bound to compound 288 -

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Basic information

Entry
Database: PDB / ID: 9gif
TitleNMDA bound to compound 288
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 / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / monoatomic cation transmembrane transport / positive regulation of reactive oxygen species biosynthetic process / 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 / excitatory synapse / monoatomic cation transport / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / calcium ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / regulation of membrane potential / excitatory postsynaptic potential / postsynaptic density membrane / brain development / visual learning / regulation of synaptic plasticity / calcium ion transmembrane transport / terminal bouton / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / response to ethanol / dendritic spine / chemical synaptic transmission / postsynaptic membrane / calmodulin binding / neuron projection / postsynaptic density / calcium ion binding / synapse / dendrite / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7343
Polymers33,4221
Non-polymers3122
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area13720 Å2
Unit cell
Length a, b, c (Å)41.85, 71.53, 96.3
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.: 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
#2: Chemical ChemComp-A1ILR / (2~{R})-2-azanyl-3-(2~{H}-thiophen-5-ylcarbonylamino)propanoic acid


Mass: 216.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→23.16 Å / Num. obs: 21502 / % possible obs: 92 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 948 / CC1/2: 0.853

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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: 1.9→23.155 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.175 / SU B: 3.166 / SU ML: 0.093 / Average fsc free: 0.9709 / Average fsc work: 0.9798 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 1040 4.843 %RANDOM
Rwork0.1773 20434 --
all0.179 ---
obs-21474 91.445 %-
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: 21.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.317 Å2-0 Å20 Å2
2--0.817 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 19 218 2463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162077
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.823141
X-RAY DIFFRACTIONr_angle_other_deg0.5451.7614805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.30459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45610375
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.77410103
X-RAY DIFFRACTIONr_chiral_restr0.0710.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.2230.2431
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21974
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21160
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21222
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2158
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.224
X-RAY DIFFRACTIONr_nbd_other0.2340.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.216
X-RAY DIFFRACTIONr_mcbond_it2.0962.0531155
X-RAY DIFFRACTIONr_mcbond_other2.0962.0531155
X-RAY DIFFRACTIONr_mcangle_it3.3123.6851443
X-RAY DIFFRACTIONr_mcangle_other3.3143.6871444
X-RAY DIFFRACTIONr_scbond_it2.5822.281156
X-RAY DIFFRACTIONr_scbond_other2.5842.2811152
X-RAY DIFFRACTIONr_scangle_it4.2234.0841696
X-RAY DIFFRACTIONr_scangle_other4.2294.0851691
X-RAY DIFFRACTIONr_lrange_it7.26825.0019691
X-RAY DIFFRACTIONr_lrange_other7.18724.7839481
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
1.9-1.9490.217590.2349900.23316720.9720.96962.73920.219
1.949-2.0020.216620.20112360.20216760.9750.97477.44630.18
2.002-2.060.229870.18814270.19116000.9650.97694.6250.165
2.06-2.1230.179610.16813930.16815660.9790.98192.8480.149
2.123-2.1920.251740.1713670.17415400.960.9893.57140.155
2.192-2.2680.187680.16712790.16814310.9740.98194.130.151
2.268-2.3520.204710.15713050.15914430.9750.98495.35690.14
2.352-2.4480.23530.16112580.16413860.9650.98394.58870.148
2.448-2.5550.222570.16611990.16913080.9730.98296.02450.152
2.555-2.6780.212450.1611100.16212630.9710.98391.44890.15
2.678-2.8210.198630.16210690.16412060.9730.98393.8640.149
2.821-2.9890.215520.17410640.17511590.9670.98196.28990.165
2.989-3.1920.223540.1719990.17410780.9670.98197.68090.167
3.192-3.4420.223540.1889470.1910200.9640.97998.13730.189
3.442-3.7620.243350.1818820.1849420.9690.97997.34610.187
3.762-4.1930.163340.1577960.1578600.9870.98596.51160.167
4.193-4.8150.169400.1496820.157640.9850.98794.50260.163
4.815-5.8340.251300.2156090.2176580.9730.97797.11250.234
5.834-8.0010.313220.2445100.2475420.9660.9798.1550.255
8.001-23.1550.239190.243120.243500.9610.96894.57140.277

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