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- PDB-5kzn: Metabotropic Glutamate Receptor -

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Basic information

Entry
Database: PDB / ID: 5kzn
TitleMetabotropic Glutamate Receptor
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 / G protein-coupled glutamate receptor signaling pathway / intracellular glutamate homeostasis / astrocyte projection / negative regulation of adenylate cyclase activity / 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 / G protein-coupled glutamate receptor signaling pathway / intracellular glutamate homeostasis / astrocyte projection / negative regulation of adenylate cyclase activity / 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 / chemical synaptic transmission / scaffold protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axon / dendrite / glutamatergic synapse / 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
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7774
Polymers63,3111
Non-polymers4673
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-5 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.850, 129.850, 252.483
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 4.84 Å3/Da / Density % sol: 74.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris HCl pH 8.5,.5% PEG MME 5K, 800mM Potassium Sodium Tartrate

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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: Feb 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→25.17 Å / Biso Wilson estimate: 109.62 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-2.9519.90.840.91100
2.95-3.1322.20.69111100
3.13-3.3522.20.4981.41100
3.35-3.6121.80.3212.11100
3.61-3.9621.30.2073.11100
3.96-4.4321.60.1245.41100
4.43-5.1121.30.0927.21100
5.11-6.26210.0887.81100
6.26-8.8520.30.0659.91100
8.85-46.75316.90.04613.7199.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.2data extraction
d*TREKdata reduction
RefinementResolution: 2.8→25.17 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9242 / SU R Cruickshank DPI: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.304 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1598 5.04 %RANDOM
Rwork0.2202 ---
obs0.2216 31717 99.99 %-
Displacement parametersBiso mean: 96 Å2
Baniso -1Baniso -2Baniso -3
1-4.4269 Å20 Å20 Å2
2--4.4269 Å20 Å2
3----8.8537 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: 1 / Resolution: 2.8→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 29 36 3908
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013978HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.175419HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1306SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes602HARMONIC5
X-RAY DIFFRACTIONt_it3978HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion19.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion518SEMIHARMONIC5
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_contact4316SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.89 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.281 155 5.39 %
Rwork0.2421 2722 -
all0.2442 2877 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -69.1479 Å / Origin y: 56.7575 Å / Origin z: 2.5106 Å
111213212223313233
T-0.2628 Å20.0172 Å20.0496 Å2-0.081 Å20.2764 Å2---0.0929 Å2
L3.7183 °2-1.3878 °2-0.0184 °2-0.7585 °20.1978 °2--0.562 °2
S-0.0823 Å °0.426 Å °0.5437 Å °0.1469 Å °0.0398 Å °0.0813 Å °-0.1868 Å °-0.0457 Å °0.0425 Å °
Refinement TLS groupSelection details: { A|* }

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