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- PDB-5kzq: Metabotropic Glutamate Receptor in complex with antagonist (1~{S}... -

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Entry
Database: PDB / ID: 5kzq
TitleMetabotropic Glutamate Receptor in complex with antagonist (1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-azanyl-3-[[3,4-bis(fluoranyl)phenyl]sulfanylmethyl]-4-oxidanyl-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid
ComponentsMetabotropic glutamate receptor 2
KeywordsSIGNALING PROTEIN / mGluR2 / antagonist / antidepressent
Function / homology
Function and homology information


regulation of response to drug / group II metabotropic glutamate receptor activity / behavioral response to nicotine / intracellular glutamate homeostasis / astrocyte projection / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate secretion / glutamate receptor activity ...regulation of response to drug / group II metabotropic glutamate receptor activity / behavioral response to nicotine / intracellular glutamate homeostasis / astrocyte projection / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate secretion / glutamate receptor activity / regulation of glutamate secretion / long-term synaptic depression / regulation of dopamine secretion / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / presynaptic modulation of chemical synaptic transmission / response to cocaine / G protein-coupled receptor activity / presynaptic membrane / gene expression / G alpha (i) signalling events / scaffold protein binding / chemical synaptic transmission / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axon / glutamatergic synapse / dendrite / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 2 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...GPCR, family 3, metabotropic glutamate receptor 2 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-6YS / Metabotropic glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsChappell, M.D. / Li, R. / Smith, S.C. / Dressman, B.A. / Tromiczak, E.G. / Tripp, A.E. / Blanco, M.-J. / Vetman, T. / Quimby, S.J. / Matt, J. ...Chappell, M.D. / Li, R. / Smith, S.C. / Dressman, B.A. / Tromiczak, E.G. / Tripp, A.E. / Blanco, M.-J. / Vetman, T. / Quimby, S.J. / Matt, J. / Britton, T. / Fivush, A.M. / Schkeryantz, J.M. / Mayhugh, D. / Erickson, J.A. / Bures, M. / Jaramillo, C. / Carpintero, M. / de Diego, J.E. / Barberis, M. / Garcia-Cerrada, S. / Soriano, J.F. / Antonysamy, S. / Atwell, S. / MacEwan, I. / Condon, B. / Bradley, C. / Wang, J. / Zhang, A. / Conners, K. / Groshong, C. / Wasserman, S.R. / Koss, J.W. / Witkin, J.M. / Li, X. / Overshiner, C. / Wafford, K.A. / Seidel, W. / Wang, X.-S. / Heinz, B.A. / Swanson, S. / Catlow, J. / Bedwell, D. / Monn, J.A. / Mitch, C.H. / Ornstein, P.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Discovery of (1S,2R,3S,4S,5R,6R)-2-Amino-3-[(3,4-difluorophenyl)sulfanylmethyl]-4-hydroxy-bicyclo[3.1.0]hexane-2,6-dicarboxylic Acid Hydrochloride (LY3020371HCl): A Potent, Metabotropic ...Title: Discovery of (1S,2R,3S,4S,5R,6R)-2-Amino-3-[(3,4-difluorophenyl)sulfanylmethyl]-4-hydroxy-bicyclo[3.1.0]hexane-2,6-dicarboxylic Acid Hydrochloride (LY3020371HCl): A Potent, Metabotropic Glutamate 2/3 Receptor Antagonist with Antidepressant-Like Activity.
Authors: Chappell, M.D. / Li, R. / Smith, S.C. / Dressman, B.A. / Tromiczak, E.G. / Tripp, A.E. / Blanco, M.J. / Vetman, T. / Quimby, S.J. / Matt, J. / Britton, T.C. / Fivush, A.M. / Schkeryantz, J.M. ...Authors: Chappell, M.D. / Li, R. / Smith, S.C. / Dressman, B.A. / Tromiczak, E.G. / Tripp, A.E. / Blanco, M.J. / Vetman, T. / Quimby, S.J. / Matt, J. / Britton, T.C. / Fivush, A.M. / Schkeryantz, J.M. / Mayhugh, D. / Erickson, J.A. / Bures, M.G. / Jaramillo, C. / Carpintero, M. / Diego, J.E. / Barberis, M. / Garcia-Cerrada, S. / Soriano, J.F. / Antonysamy, S. / Atwell, S. / MacEwan, I. / Condon, B. / Sougias, C. / Wang, J. / Zhang, A. / Conners, K. / Groshong, C. / Wasserman, S.R. / Koss, J.W. / Witkin, J.M. / Li, X. / Overshiner, C. / Wafford, K.A. / Seidel, W. / Wang, X.S. / Heinz, B.A. / Swanson, S. / Catlow, J.T. / Bedwell, D.W. / Monn, J.A. / Mitch, C.H. / Ornstein, P.L.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8913
Polymers63,3111
Non-polymers5812
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint3 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.297, 166.297, 79.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Metabotropic glutamate receptor 2 / / mGluR2


Mass: 63310.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM2, GPRC1B, MGLUR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14416
#2: Chemical ChemComp-6YS / (1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-azanyl-3-[[3,4-bis(fluoranyl)phenyl]sulfanylmethyl]-4-oxidanyl-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid


Mass: 359.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15F2NO5S
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.36 Å3/Da / Density % sol: 71.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18% PEG 20,000, 100 mM L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→47.33 Å / Num. all: 25675 / Num. obs: 25675 / % possible obs: 91.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 79.95 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.142 / Rsym value: 0.129 / Net I/av σ(I): 4.756 / Net I/σ(I): 10 / Num. measured all: 258358
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.956.30.7330.81661526310.3340.8710.7331.665.7
2.95-3.137.40.6980.92294830880.2870.8090.698281.8
3.13-3.359.40.6290.93290235050.2210.7040.6292.797.4
3.35-3.6111.30.4481.53817733700.140.4910.4484.4100
3.61-3.9611.40.2652.53510630870.0830.290.2657.499.8
3.96-4.4311.40.1395.13219528210.0430.150.13912.599.8
4.43-5.1111.30.0927.72833725020.0290.10.09217.499.8
5.11-6.2611.20.0917.62395721300.0280.0980.09118.199.5
6.26-8.8511.20.0698.71860016590.0210.0750.0692598.3
8.85-47.3310.80.0414.395218820.0120.0420.0446.892.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTER-TNT2.11.6refinement
PDB_EXTRACT3.2data extraction
d*TREKdata reduction
RefinementResolution: 2.8→32.8 Å / Cor.coef. Fo:Fc: 0.9468 / Cor.coef. Fo:Fc free: 0.9329 / SU R Cruickshank DPI: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.35 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1278 4.99 %RANDOM
Rwork0.2081 ---
obs0.2099 25607 91.13 %-
Displacement parametersBiso max: 227.27 Å2 / Biso mean: 121.14 Å2 / Biso min: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.4872 Å20 Å20 Å2
2--0.4872 Å20 Å2
3----0.9744 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: final / Resolution: 2.8→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 38 7 3747
Biso mean--114.77 74.32 -
Num. residues----503
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1190SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes585HARMONIC5
X-RAY DIFFRACTIONt_it3843HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4405SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3843HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5262HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion21.34
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.33 101 5.1 %
Rwork0.3034 1878 -
all0.3047 1979 -
obs--63.36 %
Refinement TLS params.Method: refined / Origin x: -28.9036 Å / Origin y: -26.8621 Å / Origin z: 21.3186 Å
111213212223313233
T-0.2749 Å2-0.1946 Å2-0.0606 Å2-0.0169 Å20.0921 Å2---0.3642 Å2
L4.7596 °22.1511 °2-0.4641 °2-3.0671 °2-0.4328 °2--3.0984 °2
S0.045 Å °-0.356 Å °-0.5516 Å °-0.0977 Å °-0.1621 Å °0.145 Å °0.4152 Å °-0.2869 Å °0.117 Å °
Refinement TLS groupSelection details: { A|* }

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