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- PDB-7q5i: A glucose-based molecular rotor probes the catalytic site of glyc... -

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Basic information

Entry
Database: PDB / ID: 7q5i
TitleA glucose-based molecular rotor probes the catalytic site of glycogen phosphorylase.
ComponentsGlycogen phosphorylase, muscle form
KeywordsSUGAR BINDING PROTEIN / Glycogen phosphorylase / inhibitor / type 2 diabetes / molecular rotors
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site.
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / CARBONATE ION / Chem-I0F / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNeofytos, D.D. / Chrysina, E.D.
Funding support Greece, European Union, 3items
OrganizationGrant numberCountry
Other governmentMIS 5002550 Greece
European CommissionProject ID: 653706European Union
Other governmentMIS 5048135 Greece
Citation
Journal: Org.Biomol.Chem. / Year: 2022
Title: A glucose-based molecular rotor inhibitor of glycogen phosphorylase as a probe of cellular enzymatic function.
Authors: Minadakis, M.P. / Mavreas, K.F. / Neofytos, D.D. / Paschou, M. / Kogkaki, A. / Athanasiou, V. / Mamais, M. / Veclani, D. / Iatrou, H. / Venturini, A. / Chrysina, E.D. / Papazafiri, P. / Gimisis, T.
#1: Journal: Chemistry / Year: 2017
Title: A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site.
Authors: Mamais, M. / Degli Esposti, A. / Kouloumoundra, V. / Gustavsson, T. / Monti, F. / Venturini, A. / Chrysina, E.D. / Markovitsi, D. / Gimisis, T.
History
DepositionNov 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 9, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_validate_chiral
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2866
Polymers97,6511
Non-polymers6365
Water4,522251
1
AAA: Glycogen phosphorylase, muscle form
hetero molecules

AAA: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,57212
Polymers195,3012
Non-polymers1,27110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6850 Å2
ΔGint-11 kcal/mol
Surface area56560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.602, 128.602, 116.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-1240-

HOH

21AAA-1250-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 97650.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-I0F / 2-cyano-3-[4-(dimethylamino)phenyl]-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]propanamide


Mass: 377.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6.8
Details: N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, EDTA, DTT, IMP

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→128.6 Å / Num. obs: 90796 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 31.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.4
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 4430 / CC1/2: 0.769

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MEM

5mem


Resolution: 1.8→30.002 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.562 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1805 4661 5.14 %
Rwork0.1583 86023 -
all0.159 --
obs-90684 99.961 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.558 Å2
Baniso -1Baniso -2Baniso -3
1-1.103 Å2-0 Å2-0 Å2
2--1.103 Å20 Å2
3----2.205 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 43 251 6881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176462
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6499247
X-RAY DIFFRACTIONr_angle_other_deg1.2781.58514818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65721.614409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.277151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9991559
X-RAY DIFFRACTIONr_chiral_restr0.0680.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021676
X-RAY DIFFRACTIONr_nbd_refined0.1970.21214
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.25672
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23262
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2251
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.26
X-RAY DIFFRACTIONr_nbd_other0.170.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.24
X-RAY DIFFRACTIONr_mcbond_it2.2073.7653252
X-RAY DIFFRACTIONr_mcbond_other2.2073.7633251
X-RAY DIFFRACTIONr_mcangle_it3.2085.6354067
X-RAY DIFFRACTIONr_mcangle_other3.2075.6374068
X-RAY DIFFRACTIONr_scbond_it3.1434.2743573
X-RAY DIFFRACTIONr_scbond_other3.1424.2743574
X-RAY DIFFRACTIONr_scangle_it5.0296.2345176
X-RAY DIFFRACTIONr_scangle_other5.0296.2345177
X-RAY DIFFRACTIONr_lrange_it6.46543.3127490
X-RAY DIFFRACTIONr_lrange_other6.45543.2167459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.2943460.28262630.28266100.7860.7999.98490.251
1.847-1.8970.2723390.24660900.24764290.8360.851000.21
1.897-1.9520.2463300.22359430.22462740.8840.89199.98410.185
1.952-2.0120.243230.20357460.20560690.9110.9221000.165
2.012-2.0770.2252990.18555980.18758970.9270.9391000.155
2.077-2.150.2093100.18454080.18557180.9360.9411000.154
2.15-2.230.1952910.1752490.17155400.950.9541000.143
2.23-2.3210.1962560.16450600.16553160.9520.9571000.139
2.321-2.4240.1962820.16648480.16851300.9540.9571000.148
2.424-2.5410.1932550.15946350.16148900.9550.9611000.148
2.541-2.6770.2012300.16644630.16746930.950.9581000.157
2.677-2.8380.1971940.16442290.16644230.9530.9631000.164
2.838-3.0320.2041910.1639900.16241810.9550.9651000.171
3.032-3.2730.1762320.15136730.15239050.9630.9671000.172
3.273-3.5810.1781870.14634260.14836130.9640.9691000.178
3.581-3.9960.1341730.13231240.13232970.9780.9781000.18
3.996-4.6010.1431520.12827830.12929350.9790.9821000.197
4.601-5.6020.1471370.13323750.13425120.980.9831000.226
5.602-7.7880.183810.16919240.1720060.9550.96999.95010.274
7.788-30.0020.167530.16111970.16112510.9760.9899.92010.29

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