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- PDB-2ff5: Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. ... -

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Basic information

Entry
Database: PDB / ID: 2ff5
TitleSynthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. Inhibition of PTP1B. Inhibition of and binding to glycogen phosphorylase in the crystal
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes
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. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H53 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsChrysina, E.D. / Kosmopoulou, M.N. / Leonidas, D.D. / Oikonomakos, N.G.
CitationJournal: Eur.J.Org.Chem. / Year: 2007
Title: In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C-D-Glycopyranosylbenzo(hydro)quinones Inhibition of and Binding to Glycogen Phosphorylase in the Crystal
Authors: He, L. / Zhang, Y.Z. / Tanoh, M. / Chen, G.-R. / Praly, J.-P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M. / Leonidas, D.D. / Oikonomakos, N.G.
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)97,8113
Polymers97,2911
Non-polymers5192
Water4,234235
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6216
Polymers194,5822
Non-polymers1,0394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6216
Polymers194,5822
Non-polymers1,0394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)128.173, 128.173, 115.795
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-1234-

HOH

DetailsDimeric glycogen phosphorylase is the physiologically active species

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Components

#1: Protein Glycogen phosphorylase, muscle form / E.C.2.4.1.1 / Myophosphorylase


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PYRIDOXAL-5'-PHOSPHATE bound / 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: Sugar ChemComp-H53 / (1S)-1,5-anhydro-1-(2,5-dihydroxyphenyl)-D-glucitol / 2-(2,5-DIHYDROXYPHENYL)-6-(HYDROXYMETHYL)OXANE-3,4,5-TRIOL


Type: D-saccharide / Mass: 272.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 49.66 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2003
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2.03→21.36 Å / Num. all: 61307 / Num. obs: 61307 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 32.2 Å2 / Rsym value: 0.059 / Net I/σ(I): 13.4
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 3029 / Rsym value: 0.532 / % possible all: 98.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PRJ

2prj


Resolution: 2.03→21.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3470165.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3091 5 %RANDOM
Rwork0.187 ---
all0.188 61276 --
obs0.188 61276 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.2686 Å2 / ksol: 0.360333 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.39 Å20 Å20 Å2
2--4.39 Å20 Å2
3----8.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.03→21.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 34 235 6827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 522 5.2 %
Rwork0.251 9576 -
obs-9576 98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3plp.paramplp.top
X-RAY DIFFRACTION4hl52.paramhl52.top

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