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- PDB-5cnm: mGluR3 complexed with glutamate analog -

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Basic information

Entry
Database: PDB / ID: 5cnm
TitlemGluR3 complexed with glutamate analog
ComponentsMetabotropic glutamate receptor 3
KeywordsSIGNALING PROTEIN / glutamate receptor / ligand
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / astrocyte projection / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / calcium channel regulator activity ...group II metabotropic glutamate receptor activity / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / astrocyte projection / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / calcium channel regulator activity / G protein-coupled receptor activity / presynaptic membrane / scaffold protein binding / G alpha (i) signalling events / gene expression / chemical synaptic transmission / dendritic spine / postsynaptic membrane / 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 3. / 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 ...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 3. / 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 / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / 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
Chem-52Q / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.84 Å
AuthorsMonn, J.A. / Clawson, D.K. / McKinzie, D.
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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2526
Polymers58,7771
Non-polymers4765
Water1,08160
1
A: Metabotropic glutamate receptor 3
hetero molecules

A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50412
Polymers117,5532
Non-polymers95110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.892, 99.025, 71.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metabotropic glutamate receptor 3 / mGluR3


Mass: 58776.562 Da / Num. of mol.: 1 / 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

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Non-polymers , 5 types, 65 molecules

#2: Chemical ChemComp-52Q / (1R,2S,4R,5R,6R)-2-amino-4-(1H-1,2,4-triazol-3-ylsulfanyl)bicyclo[3.1.0]hexane-2,6-dicarboxylic acid


Mass: 284.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O4S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 100mM Hepes pH 7.7 + 19% PEG 8K + 50mM Magnesium Sulfate
PH range: 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.84→71.17 Å / Num. obs: 14641 / % possible obs: 99.67 % / Redundancy: 7.2 % / Biso Wilson estimate: 62.72 Å2 / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.84→71.17 Å / Cor.coef. Fo:Fc: 0.9107 / Cor.coef. Fo:Fc free: 0.8772 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 458 3.13 %RANDOM
Rwork0.1677 ---
obs0.1697 14641 99.67 %-
Displacement parametersBiso mean: 60.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.725 Å20 Å20 Å2
2--18.7616 Å20 Å2
3----17.0366 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: 1 / Resolution: 2.84→71.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 27 60 3531
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013542HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184794HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1226SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it3542HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion21.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion460SEMIHARMONIC5
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_contact4306SEMIHARMONIC4
LS refinement shellResolution: 2.84→3.07 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2852 91 3.13 %
Rwork0.1769 2816 -
all0.1805 2907 -
obs--99.67 %

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