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- PDB-4jwx: GluN2A ligand-binding core in complex with propyl-NHP5G -

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Basic information

Entry
Database: PDB / ID: 4jwx
TitleGluN2A ligand-binding core in complex with propyl-NHP5G
ComponentsGluN2A
KeywordsUNKNOWN FUNCTION / bilobed structure
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / response to other organism ...regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / response to other organism / cellular response to magnesium ion / response to methylmercury / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / response to manganese ion / response to carbohydrate / positive regulation of inhibitory postsynaptic potential / sleep / cellular response to dsRNA / regulation of NMDA receptor activity / cellular response to lipid / locomotion / dendritic spine organization / response to amine / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / response to glycoside / NMDA selective glutamate receptor complex / voltage-gated monoatomic cation channel activity / glutamate binding / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / spinal cord development / startle response / cellular response to zinc ion / dopamine metabolic process / parallel fiber to Purkinje cell synapse / response to lithium ion / monoatomic cation transmembrane transport / cellular response to glycine / regulation of postsynaptic membrane potential / response to light stimulus / action potential / modulation of excitatory postsynaptic potential / conditioned place preference / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / neuron development / multicellular organismal response to stress / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / response to fungicide / monoatomic cation channel activity / glutamate-gated receptor activity / cellular response to manganese ion / glutamate-gated calcium ion channel activity / neurogenesis / cell adhesion molecule binding / dendrite membrane / sensory perception of pain / ionotropic glutamate receptor signaling pathway / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / protein tyrosine kinase binding / cytoplasmic vesicle membrane / synaptic membrane / sodium ion transmembrane transport / positive regulation of excitatory postsynaptic potential / response to amphetamine / learning / response to nicotine / response to cocaine / hippocampus development / protein catabolic process / synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / cellular response to amino acid stimulus / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to calcium ion / negative regulation of protein catabolic process / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / cerebral cortex development / visual learning / postsynaptic density membrane / modulation of chemical synaptic transmission / response to wounding / response to lead ion / cellular response to growth factor stimulus / calcium ion transmembrane transport / memory / calcium channel activity / terminal bouton / calcium-dependent protein binding / synaptic vesicle / calcium ion transport
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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. ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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
Chem-1N4 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHansen, K.B. / Tajima, N. / Risgaard, R. / Perszyk, R.E. / Jorgensen, L. / Vance, K.M. / Ogden, K.K. / Clausen, R.P. / Furukawa, H. / Traynelis, S.F.
CitationJournal: Mol.Pharmacol. / Year: 2013
Title: Structural determinants of agonist efficacy at the glutamate binding site of N-methyl-d-aspartate receptors.
Authors: Hansen, K.B. / Tajima, N. / Risgaard, R. / Perszyk, R.E. / Jorgensen, L. / Vance, K.M. / Ogden, K.K. / Clausen, R.P. / Furukawa, H. / Traynelis, S.F.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 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
A: GluN2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6242
Polymers31,4251
Non-polymers1991
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GluN2A
hetero molecules

A: GluN2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2484
Polymers62,8502
Non-polymers3982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3030 Å2
ΔGint-15 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.031, 52.031, 198.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GluN2A


Mass: 31425.018 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: Q00959*PLUS
#2: Chemical ChemComp-1N4 / (2R)-amino(1-hydroxy-4-propyl-1H-pyrazol-5-yl)ethanoic acid


Mass: 199.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES-NaOH, 10-18% PEG8000, 100 mM calcium acatate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 45212 / Num. obs: 44489 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.6 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FTJ

1ftj


Resolution: 1.5→19.184 Å / SU ML: 0.1 / σ(F): 1.34 / σ(I): 2 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 1895 5.09 %random
Rwork0.1597 ---
obs0.1615 37218 99.95 %-
all-37237 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 14 466 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072454
X-RAY DIFFRACTIONf_angle_d1.1453359
X-RAY DIFFRACTIONf_dihedral_angle_d13.562950
X-RAY DIFFRACTIONf_chiral_restr0.08384
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.640.20251340.17472444X-RAY DIFFRACTION100
1.64-1.68430.20691340.16842489X-RAY DIFFRACTION100
1.6843-1.73390.21881400.17272451X-RAY DIFFRACTION100
1.7339-1.78980.24181300.17332485X-RAY DIFFRACTION100
1.7898-1.85370.19821200.17262479X-RAY DIFFRACTION100
1.8537-1.92790.17831340.1652493X-RAY DIFFRACTION100
1.9279-2.01550.19781350.16352475X-RAY DIFFRACTION100
2.0155-2.12160.20061300.1582495X-RAY DIFFRACTION100
2.1216-2.25440.17171300.15992524X-RAY DIFFRACTION100
2.2544-2.42810.22531540.16472494X-RAY DIFFRACTION100
2.4281-2.67190.20931400.16432533X-RAY DIFFRACTION100
2.6719-3.05720.21081440.16832578X-RAY DIFFRACTION100
3.0572-3.84660.18161220.14442606X-RAY DIFFRACTION100
3.8466-19.18580.16511480.15012777X-RAY DIFFRACTION100

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