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- PDB-3ua8: Crystal Structure Analysis of a 6-Amino Quinazolinedione Sulfonam... -

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Basic information

Entry
Database: PDB / ID: 3ua8
TitleCrystal Structure Analysis of a 6-Amino Quinazolinedione Sulfonamide bound to human GluR2
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN/ANTAGONIST / ion channel / ionic channel / postsynaptic membrane / transmembrane / TRANSPORT PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor activity / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor activity / 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 / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / 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 / dendrite / neuronal cell body / endoplasmic reticulum membrane / signal transduction / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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-08W / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKallen, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: 6-Amino quinazolinedione sulfonamides as orally active competitive AMPA receptor antagonists.
Authors: Orain, D. / Ofner, S. / Koller, M. / Carcache, D.A. / Froestl, W. / Allgeier, H. / Rasetti, V. / Nozulak, J. / Mattes, H. / Soldermann, N. / Floersheim, P. / Desrayaud, S. / Kallen, J. / ...Authors: Orain, D. / Ofner, S. / Koller, M. / Carcache, D.A. / Froestl, W. / Allgeier, H. / Rasetti, V. / Nozulak, J. / Mattes, H. / Soldermann, N. / Floersheim, P. / Desrayaud, S. / Kallen, J. / Lingenhoehl, K. / Urwyler, S.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,3481
Non-polymers4461
Water4,396244
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5884
Polymers58,6962
Non-polymers8932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.181, 104.548, 49.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein Glutamate receptor 2 / GRIA2 / 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.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIA2, GLUR2 / Plasmid: pXI472d / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P42262
#2: Chemical ChemComp-08W / N-methyl-1-{3-[(methylsulfonyl)amino]-2,4-dioxo-7-(trifluoromethyl)-1,2,3,4-tetrahydroquinazolin-6-yl}-1H-imidazole-4-carboxamide


Mass: 446.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F3N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7.5
Details: 20% w/v 2-propanol, 10% w/v PEG4000, 100 mM HEPES, pH 7.5, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2004
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21361 / % possible obs: 98.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.062 / Χ2: 1.049 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.974.10.14121060.504199.5
1.97-2.057.30.12521100.61100
2.05-2.1411.50.11621340.7391100
2.14-2.2512.20.10221200.8791100
2.25-2.3912.60.08721280.891100
2.39-2.58130.07721650.9761100
2.58-2.8413.10.06721571.1011100
2.841-3.2512.90.05721741.2291100
3.252-4.08120.04921781.468199.2
4.082-209.80.04220891.609189.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R7X

3r7x


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2382 / WRfactor Rwork: 0.2039 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8762 / SU B: 2.815 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1625 / SU Rfree: 0.1408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 1094 5.1 %RANDOM
Rwork0.1838 ---
obs0.1854 21296 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.37 Å2 / Biso mean: 20.6273 Å2 / Biso min: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 30 244 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222085
X-RAY DIFFRACTIONr_bond_other_d0.0010.021438
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9862812
X-RAY DIFFRACTIONr_angle_other_deg0.8113.0013512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60324.14682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41115392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3781511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
X-RAY DIFFRACTIONr_mcbond_it0.591.51269
X-RAY DIFFRACTIONr_mcbond_other0.1221.5528
X-RAY DIFFRACTIONr_mcangle_it1.14622041
X-RAY DIFFRACTIONr_scbond_it1.9053816
X-RAY DIFFRACTIONr_scangle_it3.2244.5771
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 84 -
Rwork0.187 1432 -
all-1516 -
obs--99.34 %

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