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- PDB-5i58: GLUTAMATE- AND GLYCINE-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS... -

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Basic information

Entry
Database: PDB / ID: 5i58
TitleGLUTAMATE- AND GLYCINE-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH MPX-004
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist
Function / homology
Function and homology information


response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / serotonin metabolic process / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion ...response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / serotonin metabolic process / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / locomotion / response to morphine / glutamate-gated calcium ion channel activity / cellular response to dsRNA / response to carbohydrate / dendritic spine organization / regulation of monoatomic cation transmembrane transport / cellular response to lipid / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of neuronal synaptic plasticity / regulation of dendrite morphogenesis / dopamine metabolic process / regulation of axonogenesis / spinal cord development / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / ligand-gated monoatomic ion channel activity / associative learning / monoatomic cation transport / excitatory synapse / response to light stimulus / positive regulation of dendritic spine maintenance / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / glutamate receptor binding / regulation of postsynaptic membrane potential / phosphatase binding / calcium ion homeostasis / synaptic cleft / cellular response to manganese ion / prepulse inhibition / regulation of neuron apoptotic process / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / monoatomic cation channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / cell adhesion molecule binding / neurogenesis / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / learning / synaptic transmission, glutamatergic / long-term synaptic potentiation / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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 ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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-67R / GLUTAMIC ACID / GLYCINE / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsMou, T.-C. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: Neuron / Year: 2016
Title: Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors.
Authors: Yi, F. / Mou, T.C. / Dorsett, K.N. / Volkmann, R.A. / Menniti, F.S. / Sprang, S.R. / Hansen, K.B.
History
DepositionFeb 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5515
Polymers64,8732
Non-polymers6783
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-8 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.919, 86.425, 122.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33340.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31533.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959

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Non-polymers , 4 types, 92 molecules

#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: 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
#5: Chemical ChemComp-67R / 5-({[(3-chloro-4-fluorophenyl)sulfonyl]amino}methyl)-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide


Mass: 455.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15ClFN5O3S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in ...The sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in this sequence is a Ser758 in Swiss-Prot Q00959.

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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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate and 16-22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015 / Details: Miniquad Collimators
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.518→15.132 Å / Num. obs: 17895 / % possible obs: 90.5 % / Redundancy: 2.7 % / Rsym value: 0.15 / Net I/σ(I): 5.27
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.58 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NF8

4nf8


Resolution: 2.52→15.13 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.26
RfactorNum. reflection% reflection
Rfree0.292 1790 10 %
Rwork0.233 --
obs0.239 17893 89.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→15.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 43 89 4378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034421
X-RAY DIFFRACTIONf_angle_d0.6275982
X-RAY DIFFRACTIONf_dihedral_angle_d16.9342670
X-RAY DIFFRACTIONf_chiral_restr0.042661
X-RAY DIFFRACTIONf_plane_restr0.003761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5181-2.58590.421110.37361000X-RAY DIFFRACTION73
2.5859-2.66160.40161300.36241163X-RAY DIFFRACTION86
2.6616-2.7470.38711300.35631170X-RAY DIFFRACTION86
2.747-2.84460.41431320.32481189X-RAY DIFFRACTION87
2.8446-2.95770.35281320.30561198X-RAY DIFFRACTION88
2.9577-3.09120.36541350.27361211X-RAY DIFFRACTION88
3.0912-3.25260.34571370.2451230X-RAY DIFFRACTION90
3.2526-3.45420.28571410.22671266X-RAY DIFFRACTION92
3.4542-3.71720.28131410.20591276X-RAY DIFFRACTION92
3.7172-4.08460.22641470.18371319X-RAY DIFFRACTION94
4.0846-4.66050.22921460.171308X-RAY DIFFRACTION94
4.6605-5.81570.23511490.18311343X-RAY DIFFRACTION95
5.8157-15.13250.24331590.19541430X-RAY DIFFRACTION97

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