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- PDB-7onf: The binding of p-coumaroyl glucose to glycogen phosphorylase reve... -

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Basic information

Entry
Database: PDB / ID: 7onf
TitleThe binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / p-coumaroyl glucose / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTsagkarakou, A.S. / Koulas, S.M. / Kyriakis, E. / Drakou, C.E. / Leonidas, D.D.
CitationJournal: Eur J Med Chem Rep / Year: 2021
Title: Structure activity relationship of the binding of p-coumaroyl glucose to glycogen phosphorylase and its effect on hepatic cell metabolic pathways
Authors: Tsagkarakou, A.S. / Chasapi, S.A. / Koulas, S.M. / Tsialtas, I. / Kyriakis, E. / Drakou, C.E. / Kun, S. / Somsak, L. / Spyroulias, G.A. / Psarra, A.M.G. / Leonidas, D.D.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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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)96,2034
Polymers95,2811
Non-polymers9223
Water8,125451
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,4058
Polymers190,5622
Non-polymers1,8436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6860 Å2
ΔGint-31 kcal/mol
Surface area56690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.607, 128.607, 116.633
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-1439-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 95280.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical ChemComp-VKK / p-coumaroyl glucose / [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] (~{E})-3-(4-hydroxyphenyl)prop-2-enoate


Mass: 326.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 298 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: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→86.4 Å / Num. obs: 128346 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.621 / Num. unique obs: 6280 / CC1/2: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O8E

7o8e
PDB Unreleased entry


Resolution: 1.6→64.39 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 3.425 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16112 6459 5.1 %RANDOM
Rwork0.12851 ---
obs0.13014 121187 99.37 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å2-0 Å2
2--0.61 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→64.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 61 451 7101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0176872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0196504
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.8599325
X-RAY DIFFRACTIONr_angle_other_deg1.132.66514922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.685829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16321.566415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.519151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4521560
X-RAY DIFFRACTIONr_chiral_restr0.0810.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
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_it1.6123.3213259
X-RAY DIFFRACTIONr_mcbond_other1.6093.3193258
X-RAY DIFFRACTIONr_mcangle_it2.1754.9894074
X-RAY DIFFRACTIONr_mcangle_other2.1754.9914075
X-RAY DIFFRACTIONr_scbond_it2.0033.8123613
X-RAY DIFFRACTIONr_scbond_other2.0033.8123614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6725.5665241
X-RAY DIFFRACTIONr_long_range_B_refined3.48639.5797737
X-RAY DIFFRACTIONr_long_range_B_other3.28839.3347683
X-RAY DIFFRACTIONr_rigid_bond_restr1.376313376
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 454 -
Rwork0.32 8739 -
obs--97.83 %

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