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- PDB-8r6v: The complex of glycogen phosphorylase with EGCG (epigallocatechin... -

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Basic information

Entry
Database: PDB / ID: 8r6v
TitleThe complex of glycogen phosphorylase with EGCG (epigallocatechin gallate) and caffeine.
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / Phosphorylase / Inhibitor / EGCG / Caffeine
Function / homology
Function and homology information


maltodextrin phosphorylase activity / 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
CAFFEINE / Chem-KDH / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 23, 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

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,11632
Polymers96,1981
Non-polymers2,91831
Water8,539474
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,23364
Polymers192,3962
Non-polymers5,83762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)126.436, 126.436, 115.353
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-1276-

HOH

21A-1441-

HOH

31A-1470-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form


Mass: 96197.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489
#2: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: 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: isolated from a natural source / Formula: C22H18O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6.7 / Details: 10mM BES buffer pH 6.7

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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: 2.5→126.44 Å / Num. obs: 32975 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.998 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 9.4 / Num. unique obs: 3649 / CC1/2: 0.986

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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: 2.5→89.4 Å / SU B: 15.128 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.81 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23345 1572 4.8 %RANDOM
Rwork0.1613 ---
obs0.16469 31357 99.95 %-
Displacement parametersBiso mean: 25.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.61 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→89.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 163 474 7287
LS refinement shellResolution: 2.5→2.565 Å
RfactorNum. reflection% reflection
Rfree0.267 109 -
Rwork0.173 --
obs-2298 100 %

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