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- PDB-9gib: NMDA bound to compound 380 -

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Basic information

Entry
Database: PDB / ID: 9gib
TitleNMDA bound to compound 380
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 / chemical synaptic transmission / dendritic spine / 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: 1.948 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)65,8616
Polymers65,2042
Non-polymers6574
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-29 kcal/mol
Surface area24430 Å2
Unit cell
Length a, b, c (Å)53.972, 90.036, 123.174
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#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 / Production host: Escherichia coli (E. coli) / Strain (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) / References: UniProt: Q05586

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Non-polymers , 5 types, 402 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H9NO4
#5: Chemical ChemComp-A1ILP / (2~{R})-2-azanyl-3-[[3-(5-ethyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid


Mass: 321.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.21 %
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.948→72.7 Å / Num. obs: 44610 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.061 / Net I/σ(I): 8.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3252 / CC1/2: 0.613 / Rpim(I) all: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.948→72.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.749 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 2309 5.198 %RANDOM
Rwork0.2032 42114 --
all0.206 ---
obs-44423 99.46 %-
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: 29.563 Å2
Baniso -1Baniso -2Baniso -3
1--0.639 Å2-0 Å2-0 Å2
2---0.37 Å20 Å2
3---1.009 Å2
Refinement stepCycle: LAST / Resolution: 1.948→72.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 44 398 4744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164111
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.8296020
X-RAY DIFFRACTIONr_angle_other_deg0.5071.7619495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.222519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74210738
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.06910190
X-RAY DIFFRACTIONr_chiral_restr0.0730.2679
X-RAY DIFFRACTIONr_chiral_restr_other0.1630.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02999
X-RAY DIFFRACTIONr_nbd_refined0.2030.2868
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.23886
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22214
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2347
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.214
X-RAY DIFFRACTIONr_nbd_other0.1750.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.213
X-RAY DIFFRACTIONr_mcbond_it2.6272.8462223
X-RAY DIFFRACTIONr_mcbond_other2.6272.8462223
X-RAY DIFFRACTIONr_mcangle_it4.1515.1112770
X-RAY DIFFRACTIONr_mcangle_other4.155.112771
X-RAY DIFFRACTIONr_scbond_it3.1733.092217
X-RAY DIFFRACTIONr_scbond_other3.1753.0912215
X-RAY DIFFRACTIONr_scangle_it4.8745.563250
X-RAY DIFFRACTIONr_scangle_other4.8735.5593251
X-RAY DIFFRACTIONr_lrange_it7.69234.19718542
X-RAY DIFFRACTIONr_lrange_other7.69234.19618543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.948-1.9990.3591580.3142980X-RAY DIFFRACTION95.934
1.999-2.0540.311740.282960X-RAY DIFFRACTION99.6186
2.054-2.1130.291490.2562903X-RAY DIFFRACTION99.6084
2.113-2.1780.2921490.2422857X-RAY DIFFRACTION99.7346
2.178-2.250.2781490.2312783X-RAY DIFFRACTION99.5924
2.25-2.3290.261340.2162636X-RAY DIFFRACTION99.7479
2.329-2.4160.281430.2152588X-RAY DIFFRACTION99.8173
2.416-2.5150.2321410.2022477X-RAY DIFFRACTION99.5816
2.515-2.6270.2921330.2072381X-RAY DIFFRACTION99.8015
2.627-2.7550.2421290.1952283X-RAY DIFFRACTION99.7931
2.755-2.9030.2351010.192191X-RAY DIFFRACTION99.6522
2.903-3.0790.2661070.1872082X-RAY DIFFRACTION99.8176
3.079-3.2910.2391280.1871926X-RAY DIFFRACTION99.8542
3.291-3.5540.2471180.1911809X-RAY DIFFRACTION99.9481
3.554-3.8930.234920.1761698X-RAY DIFFRACTION99.8884
3.893-4.3510.187890.1561524X-RAY DIFFRACTION99.8762
4.351-5.0210.207780.1631368X-RAY DIFFRACTION99.793
5.021-6.1420.315690.2031165X-RAY DIFFRACTION99.8382
6.142-8.6550.311450.216933X-RAY DIFFRACTION99.5927
8.655-72.70.281230.206570X-RAY DIFFRACTION99.6639

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