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- PDB-9gig: NMDA bound to compound 387 -

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Basic information

Entry
Database: PDB / ID: 9gig
TitleNMDA bound to compound 387
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


glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / serotonin metabolic process / response to glycine / propylene metabolic process / sleep / Assembly and cell surface presentation of NMDA receptors ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / serotonin metabolic process / response to glycine / propylene metabolic process / sleep / 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 / startle response / monoatomic cation transmembrane transport / dopamine metabolic process / 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 / neurogenesis / EPHB-mediated forward signaling / sensory perception of pain / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / response to amphetamine / regulation of membrane potential / excitatory postsynaptic potential / protein catabolic process / postsynaptic density membrane / brain development / negative regulation of protein catabolic process / regulation of synaptic plasticity / visual learning / calcium ion transmembrane transport / response to wounding / memory / long-term synaptic potentiation / terminal bouton / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / RAF/MAP kinase cascade / response to ethanol / dendritic spine / chemical synaptic transmission / postsynaptic membrane / calmodulin binding / neuron projection / postsynaptic density / positive regulation of apoptotic process / response to xenobiotic stimulus / calcium ion binding / synapse / dendrite / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / 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 ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
B: Isoform 1 of Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6874
Polymers65,2042
Non-polymers4822
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-13 kcal/mol
Surface area24690 Å2
Unit cell
Length a, b, c (Å)54.09, 90.77, 122.88
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


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 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / Variant (production host): Origami B (DE3) / References: UniProt: G3V9C5
#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) / Variant (production host): Rosetta-gami (DE3) / References: UniProt: Q05586
#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-A1ILO / (2~{R})-2-azanyl-3-[[3-(5-ethyl-3-methyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid


Mass: 335.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H18FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
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: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.09→46.47 Å / Num. obs: 36660 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.917 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.152 / Rrim(I) all: 0.292 / Net I/σ(I): 4.3
Reflection shellResolution: 2.09→2.13 Å / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1801 / CC1/2: 0.578 / Rpim(I) all: 0.657 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→46.47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.633 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.195
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1861 5.085 %RANDOM
Rwork0.2058 34737 --
all0.208 ---
obs-36598 99.94 %-
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: 44.433 Å2
Baniso -1Baniso -2Baniso -3
1--2.307 Å2-0 Å2-0 Å2
2--0.569 Å2-0 Å2
3---1.738 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 34 104 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164109
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.8285965
X-RAY DIFFRACTIONr_angle_other_deg0.5541.7669475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.769522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50510745
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.26910189
X-RAY DIFFRACTIONr_chiral_restr0.080.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021006
X-RAY DIFFRACTIONr_nbd_refined0.2170.2775
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23586
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22166
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.210
X-RAY DIFFRACTIONr_nbd_other0.1920.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.26
X-RAY DIFFRACTIONr_mcbond_it4.014.262198
X-RAY DIFFRACTIONr_mcbond_other4.014.2612198
X-RAY DIFFRACTIONr_mcangle_it5.6017.6482737
X-RAY DIFFRACTIONr_mcangle_other5.67.6472738
X-RAY DIFFRACTIONr_scbond_it5.1184.6622205
X-RAY DIFFRACTIONr_scbond_other5.1184.6632204
X-RAY DIFFRACTIONr_scangle_it7.5518.383228
X-RAY DIFFRACTIONr_scangle_other7.558.3793229
X-RAY DIFFRACTIONr_lrange_it9.65351.43817491
X-RAY DIFFRACTIONr_lrange_other9.65351.45317456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.1440.3291220.2882533X-RAY DIFFRACTION99.9247
2.144-2.2030.2771310.2542476X-RAY DIFFRACTION99.9617
2.203-2.2670.2731110.2412411X-RAY DIFFRACTION100
2.267-2.3360.2661210.2512322X-RAY DIFFRACTION99.9591
2.336-2.4130.31290.2382250X-RAY DIFFRACTION99.916
2.413-2.4970.3071210.2382184X-RAY DIFFRACTION99.9566
2.497-2.5910.3091200.2242131X-RAY DIFFRACTION99.9556
2.591-2.6960.3141190.222022X-RAY DIFFRACTION99.9533
2.696-2.8160.283990.21948X-RAY DIFFRACTION99.9512
2.816-2.9530.247900.1971885X-RAY DIFFRACTION99.9494
2.953-3.1120.2281000.1861802X-RAY DIFFRACTION100
3.112-3.30.269950.181686X-RAY DIFFRACTION99.9439
3.3-3.5260.231970.1891611X-RAY DIFFRACTION99.9415
3.526-3.8070.216880.1961479X-RAY DIFFRACTION100
3.807-4.1670.226640.1821402X-RAY DIFFRACTION99.9318
4.167-4.6550.233770.1731247X-RAY DIFFRACTION99.9245
4.655-5.3660.201550.1841139X-RAY DIFFRACTION100
5.366-6.550.285530.234962X-RAY DIFFRACTION100
6.55-9.1720.306450.215771X-RAY DIFFRACTION99.8776
9.172-46.470.272240.236476X-RAY DIFFRACTION99.6016

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