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- PDB-3lsf: Piracetam bound to the ligand binding domain of GluA2 -

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Basic information

Entry
Database: PDB / ID: 3lsf
TitlePiracetam bound to the ligand binding domain of GluA2
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / glutamate receptor / GluR2 / GluA2 / AMPA receptor / neurotransmitter receptor / S1S2 / allosteric modulator / Alternative splicing / Cell junction / Cell membrane / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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 / 2-(2-oxopyrrolidin-1-yl)acetamide / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsAhmed, A.H. / Ptak, C.P. / 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 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: 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 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutamate receptor 2
E: Glutamate receptor 2
H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,04617
Polymers86,4253
Non-polymers1,62114
Water15,619867
1
B: Glutamate receptor 2
E: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,67611
Polymers57,6172
Non-polymers1,0599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-43 kcal/mol
Surface area23100 Å2
MethodPISA
2
H: Glutamate receptor 2
hetero molecules

H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74112
Polymers57,6172
Non-polymers1,12510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_566x,-y+1,-z+11
Buried area2400 Å2
ΔGint-86 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.275, 114.023, 163.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 28808.297 Da / Num. of mol.: 3 / Mutation: N242S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


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


Mass: 142.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N2O2 / Comment: medication*YM
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.84 %
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: Mar 30, 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: 1.85→50 Å / Num. obs: 71963 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 22.593
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.186 / Rsym value: 0.532 / % possible all: 88

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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: 1.851→33.255 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / σ(F): 0.11 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 1918 2.67 %
Rwork0.1962 --
obs0.1971 71963 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.844 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 3.49 Å2
Baniso -1Baniso -2Baniso -3
1--6.6296 Å2-6.051 Å2-4.8038 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.851→33.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6047 0 125 867 7039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076268
X-RAY DIFFRACTIONf_angle_d1.0738417
X-RAY DIFFRACTIONf_dihedral_angle_d15.3822307
X-RAY DIFFRACTIONf_chiral_restr0.07921
X-RAY DIFFRACTIONf_plane_restr0.0071054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.851-1.89710.2702990.23173775X-RAY DIFFRACTION71
1.8971-1.94840.2981180.21674368X-RAY DIFFRACTION84
1.9484-2.00570.24521330.20994651X-RAY DIFFRACTION89
2.0057-2.07050.26511360.18684921X-RAY DIFFRACTION94
2.0705-2.14450.21881380.18235032X-RAY DIFFRACTION95
2.1445-2.23030.2151400.18145053X-RAY DIFFRACTION96
2.2303-2.33180.25211400.18875100X-RAY DIFFRACTION96
2.3318-2.45470.25881400.19865112X-RAY DIFFRACTION97
2.4547-2.60840.22191430.20025173X-RAY DIFFRACTION98
2.6084-2.80970.24971410.20145247X-RAY DIFFRACTION98
2.8097-3.09230.21211470.19775293X-RAY DIFFRACTION99
3.0923-3.53930.18571450.18095300X-RAY DIFFRACTION99
3.5393-4.45750.21611460.17265404X-RAY DIFFRACTION99
4.4575-33.26070.21011520.21435616X-RAY DIFFRACTION99

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