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- PDB-5cnk: mglur3 with glutamate -

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Basic information

Entry
Database: PDB / ID: 5cnk
Titlemglur3 with glutamate
ComponentsMetabotropic glutamate receptor 3
KeywordsSIGNALING PROTEIN / glutamate receptor
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / G protein-coupled receptor activity ...group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / G protein-coupled receptor activity / presynaptic membrane / gene expression / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 3 / 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 3 / 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. / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / IODIDE ION / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsMonn, J.A. / Clawson, D.K.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Synthesis and Pharmacological Characterization of C4-(Thiotriazolyl)-substituted-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylates. Identification of (1R,2S,4R,5R,6R)-2-Amino-4-(1H-1,2,4-triazol- ...Title: Synthesis and Pharmacological Characterization of C4-(Thiotriazolyl)-substituted-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylates. Identification of (1R,2S,4R,5R,6R)-2-Amino-4-(1H-1,2,4-triazol-3-ylsulfanyl)bicyclo[3.1.0]hexane-2,6-dicarboxylic Acid (LY2812223), a Highly Potent, Functionally Selective mGlu2 Receptor Agonist.
Authors: Monn, J.A. / Prieto, L. / Taboada, L. / Hao, J. / Reinhard, M.R. / Henry, S.S. / Beadle, C.D. / Walton, L. / Man, T. / Rudyk, H. / Clark, B. / Tupper, D. / Baker, S.R. / Lamas, C. / Montero, ...Authors: Monn, J.A. / Prieto, L. / Taboada, L. / Hao, J. / Reinhard, M.R. / Henry, S.S. / Beadle, C.D. / Walton, L. / Man, T. / Rudyk, H. / Clark, B. / Tupper, D. / Baker, S.R. / Lamas, C. / Montero, C. / Marcos, A. / Blanco, J. / Bures, M. / Clawson, D.K. / Atwell, S. / Lu, F. / Wang, J. / Russell, M. / Heinz, B.A. / Wang, X. / Carter, J.H. / Getman, B.G. / Catlow, J.T. / Swanson, S. / Johnson, B.G. / Shaw, D.B. / McKinzie, D.L.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 2.0Feb 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_oper_list / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 3
B: Metabotropic glutamate receptor 3
C: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,74614
Polymers176,3303
Non-polymers1,41611
Water39622
1
A: Metabotropic glutamate receptor 3
hetero molecules

A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,86312
Polymers117,5532
Non-polymers1,30910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Metabotropic glutamate receptor 3
hetero molecules

C: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3158
Polymers117,5532
Non-polymers7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
3
C: Metabotropic glutamate receptor 3
hetero molecules

B: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3158
Polymers117,5532
Non-polymers7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
4
A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4316
Polymers58,7771
Non-polymers6555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1574
Polymers58,7771
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
C: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1574
Polymers58,7771
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.344, 80.004, 206.861
Angle α, β, γ (deg.)90.00, 130.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metabotropic glutamate receptor 3 / / mGluR3


Mass: 58776.562 Da / Num. of mol.: 3 / Fragment: UNP residues 2-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM3, GPRC1C, MGLUR3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14832
#2: 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
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 16% PEG 3350 + 200mM Ammonium Iodide, 50mM Tris pH 8.0 / 150mM NaCl
PH range: pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.15→78.38 Å / Num. obs: 29288 / % possible obs: 97.85 % / Redundancy: 3.6 % / Biso Wilson estimate: 75.83 Å2 / Net I/σ(I): 3.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 3.15→78.38 Å / Cor.coef. Fo:Fc: 0.826 / Cor.coef. Fo:Fc free: 0.7801 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.472
RfactorNum. reflection% reflectionSelection details
Rfree0.258 873 2.98 %RANDOM
Rwork0.2211 ---
obs0.2222 29288 97.85 %-
Displacement parametersBiso mean: 55.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.8094 Å20 Å20.5178 Å2
2---4.4597 Å20 Å2
3---3.6504 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: 1 / Resolution: 3.15→78.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10521 0 20 22 10563
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110757HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.214551HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3723SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes273HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1569HARMONIC5
X-RAY DIFFRACTIONt_it10757HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion21.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1391SEMIHARMONIC5
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_contact11991SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.26 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2767 92 3.22 %
Rwork0.2302 2765 -
all0.2317 2857 -
obs--97.85 %

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