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- PDB-3lsx: Piracetam bound to the ligand binding domain of GluA3 -

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Basic information

Entry
Database: PDB / ID: 3lsx
TitlePiracetam bound to the ligand binding domain of GluA3
ComponentsGluA3 S1S2 domain
KeywordsTRANSPORT PROTEIN / glutamate receptor / GluR3 / GluA3 / AMPA receptor / neurotransmitter receptor / S1S2 / allosteric modulator
Function / homology
Function and homology information


Activation of AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / chemical synaptic transmission, postsynaptic / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / chemical synaptic transmission, postsynaptic / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / presynaptic active zone membrane / synaptic cleft / glutamate-gated receptor activity / response to fungicide / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / membrane / 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
GLUTAMIC ACID / 2-(2-oxopyrrolidin-1-yl)acetamide / Glutamate receptor 3 / Glutamate receptor 3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsAhmed, A.H. / Oswald, R.E.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Piracetam Defines a New Binding Site for Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazole-propionic Acid (AMPA) Receptors.
Authors: Ahmed, A.H. / Oswald, R.E.
History
DepositionFeb 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: GluA3 S1S2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3114
Polymers28,9561
Non-polymers3553
Water6,323351
1
A: GluA3 S1S2 domain
hetero molecules

A: GluA3 S1S2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6228
Polymers57,9132
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2020 Å2
ΔGint-52 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.364, 47.655, 137.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-295-

HOH

21A-306-

HOH

31A-312-

HOH

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Components

#1: Protein GluA3 S1S2 domain


Mass: 28956.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat), (gene. exp.) MUS MUSCULUS (house mouse)
Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19492, UniProt: Q9Z2W9
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-PZI / 2-(2-oxopyrrolidin-1-yl)acetamide / Piracetam


Mass: 142.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O2 / Comment: medication*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18% PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 M zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2009
RadiationMonochromator: RH COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19729 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 18.093
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3 / Rsym value: 0.478 / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DP6

3dp6


Resolution: 2.006→45.044 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / σ(F): 0.1 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1886 9.56 %
Rwork0.1684 --
obs0.1736 19729 90.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.045 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0703 Å2-0 Å20 Å2
2---1.6904 Å2-0 Å2
3---0.6201 Å2
Refinement stepCycle: LAST / Resolution: 2.006→45.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 21 351 2403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132112
X-RAY DIFFRACTIONf_angle_d1.4572843
X-RAY DIFFRACTIONf_dihedral_angle_d16.514787
X-RAY DIFFRACTIONf_chiral_restr0.095312
X-RAY DIFFRACTIONf_plane_restr0.006356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.006-2.05970.22411220.17131159X-RAY DIFFRACTION78
2.0597-2.12030.23851340.16611269X-RAY DIFFRACTION86
2.1203-2.18880.23211350.16761260X-RAY DIFFRACTION86
2.1888-2.2670.22821380.16881277X-RAY DIFFRACTION85
2.267-2.35780.23391330.17731302X-RAY DIFFRACTION88
2.3578-2.46510.26031360.18381316X-RAY DIFFRACTION89
2.4651-2.5950.23911420.18021356X-RAY DIFFRACTION90
2.595-2.75760.24411430.17111376X-RAY DIFFRACTION92
2.7576-2.97050.24461530.1681418X-RAY DIFFRACTION94
2.9705-3.26930.20731540.1691460X-RAY DIFFRACTION97
3.2693-3.74220.20141600.15471520X-RAY DIFFRACTION99
3.7422-4.7140.19781630.14191532X-RAY DIFFRACTION99
4.714-45.05550.20131730.17621598X-RAY DIFFRACTION98

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