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- PDB-5tpa: Structure of the human GluN1/GluN2A LBD in complex with compound ... -

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Basic information

Entry
Database: PDB / ID: 5tpa
TitleStructure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / NMDA receptor / glutamate / glycine / calcium channel / membrane
Function / homology
Function and homology information


excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / activation of cysteine-type endopeptidase activity / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / regulation of monoatomic cation transmembrane transport ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / activation of cysteine-type endopeptidase activity / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / glutamate binding / glutamate receptor signaling pathway / protein heterotetramerization / positive regulation of calcium ion transport into cytosol / positive regulation of reactive oxygen species biosynthetic process / glycine binding / startle response / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / dopamine metabolic process / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / monoatomic cation transport / Long-term potentiation / excitatory synapse / ligand-gated monoatomic ion channel activity / positive regulation of excitatory postsynaptic potential / calcium ion homeostasis / synaptic cleft / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / sensory perception of pain / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / neurogenesis / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / synaptic membrane / long-term synaptic potentiation / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / brain development / visual learning / cytoplasmic vesicle membrane / protein catabolic process / regulation of synaptic plasticity / negative regulation of protein catabolic process / terminal bouton / memory / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / neuron projection / positive regulation of apoptotic process / response to xenobiotic stimulus / glutamatergic synapse / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7H2 / GLUTAMIC ACID / GLYCINE / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsWallweber, H.J.A. / Lupardus, P.J.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: GluN2A-Selective Pyridopyrimidinone Series of NMDAR Positive Allosteric Modulators with an Improved in Vivo Profile.
Authors: Villemure, E. / Volgraf, M. / Jiang, Y. / Wu, G. / Ly, C.Q. / Yuen, P.W. / Lu, A. / Luo, X. / Liu, M. / Zhang, S. / Lupardus, P.J. / Wallweber, H.J. / Liederer, B.M. / Deshmukh, G. / Plise, ...Authors: Villemure, E. / Volgraf, M. / Jiang, Y. / Wu, G. / Ly, C.Q. / Yuen, P.W. / Lu, A. / Luo, X. / Liu, M. / Zhang, S. / Lupardus, P.J. / Wallweber, H.J. / Liederer, B.M. / Deshmukh, G. / Plise, E. / Tay, S. / Wang, T.M. / Hanson, J.E. / Hackos, D.H. / Scearce-Levie, K. / Schwarz, J.B. / Sellers, B.D.
History
DepositionOct 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 2A
B: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9225
Polymers65,2932
Non-polymers6303
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-3 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.757, 90.239, 122.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / hNR2A


Mass: 31883.441 Da / Num. of mol.: 1
Fragment: Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12879
#2: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33409.074 Da / Num. of mol.: 1
Fragment: UNP residues 394-544, GT linker, UNP residues 663-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05586

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Non-polymers , 4 types, 150 molecules

#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-7H2 / (1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile


Mass: 407.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13ClF3N5O
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2014
RadiationMonochromator: liquid nitrogen-cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→122.66 Å / Num. obs: 22726 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 62.31 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.6
Reflection shellHighest resolution: 2.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→72.69 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.466 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.507 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1154 5.1 %RANDOM
Rwork0.187 ---
obs0.19 22620 100 %-
Displacement parametersBiso mean: 55.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.7756 Å20 Å20 Å2
2--4.9828 Å20 Å2
3----2.2072 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.48→72.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 43 147 4523
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014491HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146084HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1557SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes671HARMONIC5
X-RAY DIFFRACTIONt_it4491HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion18.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion593SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5163SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.316 150 5.09 %
Rwork0.216 2798 -
all0.221 2948 -
obs--100 %

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