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- PDB-9gid: NMDA bound to compound 338 -

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Basic information

Entry
Database: PDB / ID: 9gid
TitleNMDA bound to compound 338
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 / Neurexins and neuroligins / 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 / Neurexins and neuroligins / neurotransmitter receptor complex / 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 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / monoatomic ion channel complex / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / sodium ion transmembrane transport / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / synaptic membrane / postsynaptic density membrane / terminal bouton / brain development / visual learning / calcium ion transmembrane transport / regulation of synaptic plasticity / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / dendritic spine / response to ethanol / postsynaptic membrane / calmodulin binding / neuron projection / 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: 2 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)33,9774
Polymers33,4221
Non-polymers5553
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-31 kcal/mol
Surface area13580 Å2
Unit cell
Length a, b, c (Å)41.56, 72.5, 95.79
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-A1ILT / (2~{R})-2-azanyl-3-[(7-bromanyl-4-fluoranyl-3~{H}-1-benzothiophen-2-yl)carbonylamino]propanoic acid


Mass: 363.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12BrFN2O3S / 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.: 161 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
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: 2→23.96 Å / Num. obs: 45513 / % possible obs: 95.1 % / Redundancy: 2.4 % / CC1/2: 0.974 / Rmerge(I) obs: 0.171 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1113 / CC1/2: 0.478

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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: 2→23.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.551 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 993 5.202 %RANDOM
Rwork0.2061 18097 --
all0.209 ---
obs-19090 94.379 %-
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: 23.026 Å2
Baniso -1Baniso -2Baniso -3
1-0.246 Å20 Å2-0 Å2
2--0.37 Å20 Å2
3----0.616 Å2
Refinement stepCycle: LAST / Resolution: 2→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 30 161 2414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162066
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.8213134
X-RAY DIFFRACTIONr_angle_other_deg0.5351.764778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.89959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96910371
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.12410100
X-RAY DIFFRACTIONr_chiral_restr0.0720.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_nbd_refined0.2030.2473
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21978
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21156
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1190.219
X-RAY DIFFRACTIONr_nbd_other0.2280.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2380.210
X-RAY DIFFRACTIONr_mcbond_it2.1642.251151
X-RAY DIFFRACTIONr_mcbond_other2.1612.251151
X-RAY DIFFRACTIONr_mcangle_it3.3874.0361437
X-RAY DIFFRACTIONr_mcangle_other3.3864.0371438
X-RAY DIFFRACTIONr_scbond_it2.5542.4381155
X-RAY DIFFRACTIONr_scbond_other2.5112.431146
X-RAY DIFFRACTIONr_scangle_it3.9754.3981697
X-RAY DIFFRACTIONr_scangle_other3.9474.3781686
X-RAY DIFFRACTIONr_lrange_it6.62727.289601
X-RAY DIFFRACTIONr_lrange_other6.59727.2319497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.349520.3341054X-RAY DIFFRACTION76.1184
2.052-2.1070.314660.2991106X-RAY DIFFRACTION83.5949
2.107-2.1680.272620.2631271X-RAY DIFFRACTION95.6927
2.168-2.2340.345760.2481231X-RAY DIFFRACTION97.5373
2.234-2.3070.32600.231247X-RAY DIFFRACTION97.976
2.307-2.3870.237510.211180X-RAY DIFFRACTION98.2442
2.387-2.4760.302670.2381138X-RAY DIFFRACTION98.127
2.476-2.5760.312770.2231076X-RAY DIFFRACTION98.0442
2.576-2.6890.278560.2121051X-RAY DIFFRACTION98.0514
2.689-2.8190.325590.186997X-RAY DIFFRACTION95.6522
2.819-2.9690.256560.18973X-RAY DIFFRACTION98.0934
2.969-3.1460.199430.177910X-RAY DIFFRACTION97.5435
3.146-3.3590.21550.182855X-RAY DIFFRACTION97.6395
3.359-3.6220.217430.182810X-RAY DIFFRACTION96.9318
3.622-3.9590.238300.166747X-RAY DIFFRACTION96.6418
3.959-4.4110.184440.16672X-RAY DIFFRACTION96.3661
4.411-5.0650.313340.163598X-RAY DIFFRACTION95.1807
5.065-6.1350.219320.229516X-RAY DIFFRACTION94.6459
6.135-8.4060.248200.225412X-RAY DIFFRACTION93.3045
8.406-23.960.179100.204253X-RAY DIFFRACTION85.1133

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