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- PDB-3lsl: Piracetam bound to the ligand binding domain of GluA2 (flop form) -

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Basic information

Entry
Database: PDB / ID: 3lsl
TitlePiracetam bound to the ligand binding domain of GluA2 (flop form)
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 cytoplasm / cellular response to amine stimulus / dendritic spine head / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor clustering / cellular response to glycine / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / immunoglobulin binding / asymmetric synapse / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / conditioned place preference / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated receptor activity / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / dendrite membrane / excitatory synapse / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / synaptic membrane / positive regulation of excitatory postsynaptic potential / dendritic shaft / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / protein tetramerization / establishment of protein localization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / postsynaptic density membrane / receptor internalization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / synaptic vesicle membrane / signaling receptor activity / amyloid-beta binding / presynapse / growth cone / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex 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. / Periplasmic binding protein-like II / Receptor, 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. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 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: 2.122 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 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 1.3Sep 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_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.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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
D: Glutamate receptor 2
G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,55420
Polymers86,5063
Non-polymers2,04817
Water9,044502
1
A: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,07914
Polymers57,6712
Non-polymers1,40912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-62 kcal/mol
Surface area22810 Å2
MethodPISA
2
G: Glutamate receptor 2
hetero molecules

G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,94912
Polymers57,6712
Non-polymers1,27810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554x,-y,-z-11
Buried area2320 Å2
ΔGint-47 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.528, 114.343, 163.829
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: 28835.320 Da / Num. of mol.: 3
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.: 9 / 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.: 502 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
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: Oct 18, 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: 2.1→50 Å / Num. obs: 43568 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 16.599
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.172 / Num. unique all: 2142 / Rsym value: 0.328 / % possible all: 84.3

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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: 2.122→46.882 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 1908 4.38 %RANDOM
Rwork0.2007 ---
obs0.2034 43568 84.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.506 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.7066 Å2-0.2681 Å21.9747 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.122→46.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 155 502 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136271
X-RAY DIFFRACTIONf_angle_d1.5118423
X-RAY DIFFRACTIONf_dihedral_angle_d17.3542355
X-RAY DIFFRACTIONf_chiral_restr0.094914
X-RAY DIFFRACTIONf_plane_restr0.0171061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.122-2.17510.33551110.23792306X-RAY DIFFRACTION66
2.1751-2.23390.29621300.22262687X-RAY DIFFRACTION78
2.2339-2.29960.25261210.21612793X-RAY DIFFRACTION81
2.2996-2.37380.29221310.21892957X-RAY DIFFRACTION84
2.3738-2.45870.32671330.22112964X-RAY DIFFRACTION86
2.4587-2.55710.26321380.21933033X-RAY DIFFRACTION87
2.5571-2.67350.32451440.2063092X-RAY DIFFRACTION88
2.6735-2.81440.27181480.20613147X-RAY DIFFRACTION90
2.8144-2.99070.25771410.2043142X-RAY DIFFRACTION90
2.9907-3.22160.30041440.20863119X-RAY DIFFRACTION89
3.2216-3.54570.27541420.18633100X-RAY DIFFRACTION88
3.5457-4.05850.21551410.17253075X-RAY DIFFRACTION87
4.0585-5.11230.19321430.15623125X-RAY DIFFRACTION87
5.1123-46.89340.25981410.21913120X-RAY DIFFRACTION82

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