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- PDB-8r53: The complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3... -

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Basic information

Entry
Database: PDB / ID: 8r53
TitleThe complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3-gallate (EGCG) and glucose.
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / Glycogen Phosphorylase / Glucose / Epigallocatechin-3-Gallate
Function / homology
Function and homology information


glycogen phosphorylase / glycogen 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
alpha-D-glucopyranose / Chem-KDH / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlexopoulos, S. / Papakostopoulou, S. / Koulas, M.S. / Leonidas, D.D. / Skamnaki, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Evidence for the Quercetin Binding Site of Glycogen Phosphorylase as a Target for Liver-Isoform-Selective Inhibitors against Glioblastoma: Investigation of Flavanols Epigallocatechin Gallate and Epigallocatechin.
Authors: Alexopoulos, S. / McGawley, M. / Mathews, R. / Papakostopoulou, S. / Koulas, S. / Leonidas, D.D. / Zwain, T. / Hayes, J.M. / Skamnaki, V.
History
DepositionNov 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,86829
Polymers96,1981
Non-polymers2,67028
Water14,790821
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,73658
Polymers192,3962
Non-polymers5,34056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)126.183, 126.183, 115.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1151-

HOH

21A-1393-

HOH

31A-1474-

HOH

41A-1534-

HOH

51A-1682-

HOH

61A-1752-

HOH

71A-1802-

HOH

81A-1805-

HOH

91A-1821-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 96197.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-KDH / (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate / (-)-Epigallocatechin-3-gallate / EGCG


Mass: 458.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18O11 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6.7 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 100 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 / Detector: PIXEL / Date: Mar 14, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→126.18 Å / Num. obs: 63292 / % possible obs: 99.97 % / Redundancy: 9.3 % / CC1/2: 0.99 / Net I/σ(I): 27.4
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 10.8 / Num. unique obs: 4389 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267phasing
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→85.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.422 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19729 3142 5 %RANDOM
Rwork0.15509 ---
obs0.15723 60075 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.704 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→85.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 149 821 7619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136966
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156691
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6489408
X-RAY DIFFRACTIONr_angle_other_deg1.381.58115294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07121.394416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.965151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5851563
X-RAY DIFFRACTIONr_chiral_restr0.0830.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3282.693273
X-RAY DIFFRACTIONr_mcbond_other2.3282.6883272
X-RAY DIFFRACTIONr_mcangle_it3.1784.0184091
X-RAY DIFFRACTIONr_mcangle_other3.1784.024092
X-RAY DIFFRACTIONr_scbond_it3.4323.1353693
X-RAY DIFFRACTIONr_scbond_other3.4223.133689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.84.5385315
X-RAY DIFFRACTIONr_long_range_B_refined6.73632.7598272
X-RAY DIFFRACTIONr_long_range_B_other6.73532.768273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 230 -
Rwork0.187 4350 -
obs--100 %

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