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- PDB-3r7x: Crystal Structure Analysis of a Quinazolinedione sulfonamide boun... -

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Basic information

Entry
Database: PDB / ID: 3r7x
TitleCrystal Structure Analysis of a Quinazolinedione sulfonamide bound to human GluR2: A Novel Class of Competitive AMPA Receptor Antagonists with Oral Activity
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / ion channel / ionic channel / postsynaptic membrane / transmembrane
Function / homology
Function and homology information


Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / chemical synaptic transmission / postsynapse / dendritic spine / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / signal transduction / plasma membrane
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. / Receptor, ligand binding region / Receptor family ligand binding region ...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
GLUTAMIC ACID / Chem-QSN / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKallen, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Quinazolinedione sulfonamides: A novel class of competitive AMPA receptor antagonists with oral activity.
Authors: Koller, M. / Lingenhoehl, K. / Schmutz, M. / Vranesic, I.T. / Kallen, J. / Auberson, Y.P. / Carcache, D.A. / Mattes, H. / Ofner, S. / Orain, D. / Urwyler, S.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2094
Polymers58,6962
Non-polymers5132
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-9 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.360, 88.578, 97.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29347.865 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pXI472d / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P42262
#2: Chemical ChemComp-QSN / N-[6-(1H-imidazol-1-yl)-7-nitro-2,4-dioxo-1,4-dihydroquinazolin-3(2H)-yl]methanesulfonamide


Mass: 366.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N6O6S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 413-527 CONNECTED TO UNP RESIDUES 653-796 VIA AN ...PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 413-527 CONNECTED TO UNP RESIDUES 653-796 VIA AN ENGINEERED GT LINKER

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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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 200 mM ammonium acetate, 28% PEG4000, pH 4.6, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8
DetectorType: MAR / Detector: CCD / Date: Sep 9, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 29462 / Num. obs: 29462 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Χ2: 1.079 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.172.30.10827830.382195.6
2.17-2.264.60.1129250.4081100
2.26-2.365.50.10229140.4481100
2.36-2.495.50.09229280.5721100
2.49-2.645.40.0829390.6691100
2.64-2.855.50.07429470.8521100
2.85-3.135.40.0729581.1361100
3.13-3.595.30.06629841.6021100
3.59-4.5150.05830052.007199.8
4.51-204.70.05230792.307197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2617 / WRfactor Rwork: 0.2202 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.84 / SU B: 4.944 / SU ML: 0.135 / SU R Cruickshank DPI: 0.2973 / SU Rfree: 0.2161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1491 5.1 %RANDOM
Rwork0.2041 ---
all0.2064 29411 --
obs0.2064 29411 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.27 Å2 / Biso mean: 23.5406 Å2 / Biso min: 5.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 35 446 4529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224158
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9825597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2785514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50324.217166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33915791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213029
X-RAY DIFFRACTIONr_mcbond_it0.511.52552
X-RAY DIFFRACTIONr_mcangle_it0.95824104
X-RAY DIFFRACTIONr_scbond_it1.42731606
X-RAY DIFFRACTIONr_scangle_it2.3764.51493
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 104 -
Rwork0.199 1905 -
all-2009 -
obs--93.75 %

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