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- PDB-9gic: NMDA bound to compound 345 -

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Basic information

Entry
Database: PDB / ID: 9gic
TitleNMDA bound to compound 345
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 / neurotransmitter receptor complex / NMDA selective glutamate 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 / neurotransmitter receptor complex / NMDA selective glutamate 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 / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / Ras activation upon Ca2+ influx through NMDA receptor / excitatory postsynaptic potential / regulation of membrane potential / synaptic membrane / 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 / neuron projection / calmodulin binding / postsynaptic density / synapse / dendrite / 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 / MOLECULAR REPLACEMENT / Resolution: 1.823 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)33,9214
Polymers33,4221
Non-polymers4993
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-31 kcal/mol
Surface area13770 Å2
Unit cell
Length a, b, c (Å)41.96, 70.745, 96
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-A1ILQ / (2~{R})-2-azanyl-3-[[3-(phenylmethyl)-2~{H}-thiophen-5-yl]carbonylamino]propanoic acid


Mass: 306.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
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: Jan 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.82→20.57 Å / Num. obs: 2553444 / % possible obs: 97.5 % / Redundancy: 6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.8
Reflection shellResolution: 1.82→1.86 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 6489 / CC1/2: 0.91

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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: 1.823→20.566 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.202 / SU B: 2.565 / SU ML: 0.081 / Average fsc free: 0.9707 / Average fsc work: 0.9786 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1232 4.835 %RANDOM
Rwork0.1906 24248 --
all0.192 ---
obs-25480 97.2 %-
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: 18.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.817 Å20 Å2-0 Å2
2--0.691 Å20 Å2
3---0.126 Å2
Refinement stepCycle: LAST / Resolution: 1.823→20.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 31 171 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162091
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.8023148
X-RAY DIFFRACTIONr_angle_other_deg0.5751.7534835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7635289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.4958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50510376
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4310101
X-RAY DIFFRACTIONr_chiral_restr0.0820.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.2080.2414
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21954
X-RAY DIFFRACTIONr_nbtor_refined0.180.21173
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2140
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.213
X-RAY DIFFRACTIONr_nbd_other0.2010.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.211
X-RAY DIFFRACTIONr_mcbond_it1.8471.7571153
X-RAY DIFFRACTIONr_mcbond_other1.8471.7571153
X-RAY DIFFRACTIONr_mcangle_it2.9233.1531440
X-RAY DIFFRACTIONr_mcangle_other2.9233.1531441
X-RAY DIFFRACTIONr_scbond_it2.6651.981164
X-RAY DIFFRACTIONr_scbond_other2.6061.981157
X-RAY DIFFRACTIONr_scangle_it4.1863.5351707
X-RAY DIFFRACTIONr_scangle_other4.1583.5321696
X-RAY DIFFRACTIONr_lrange_it6.33821.0999620
X-RAY DIFFRACTIONr_lrange_other6.29521.0139491
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
1.823-1.870.224790.22217220.22318630.970.97396.6720.209
1.87-1.9210.232700.19517400.19718600.9660.97797.31180.179
1.921-1.9760.18780.16716990.16817960.9820.98398.94210.155
1.976-2.0360.24840.17416110.17717310.9590.9897.92030.164
2.036-2.1020.229970.17915560.18217140.9720.9896.44110.17
2.102-2.1750.206780.17515270.17616290.9730.98198.52670.169
2.175-2.2560.235760.17314710.17615890.9680.98197.35680.171
2.256-2.3470.179700.16714080.16715470.9840.98295.53980.165
2.347-2.450.2560.1713520.17114630.9740.98196.24060.172
2.45-2.5680.197720.1712830.17214000.9710.98296.78570.173
2.568-2.7050.246770.17312300.17613520.9660.98196.67160.183
2.705-2.8650.228560.19111640.19312710.9670.97795.98740.2
2.865-3.0590.229720.19411040.19612220.9620.97596.23570.207
3.059-3.2980.242540.20110500.20311350.9680.97497.26870.223
3.298-3.6040.178480.2049820.20310530.9820.97797.81580.223
3.604-4.0140.245470.1868910.1899550.9670.9898.21990.214
4.014-4.6050.201410.1728150.1738670.9780.98298.73130.213
4.605-5.5710.229320.2176890.2187340.9820.97998.22890.28
5.571-7.6050.282280.2915720.2916050.9570.95899.17360.352
7.605-20.5660.237170.2523820.2514030.9680.96899.00740.311

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