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- PDB-6y5c: The crystal structure of glycogen phosphorylase in complex with 52 -

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Basic information

Entry
Database: PDB / ID: 6y5c
TitleThe crystal structure of glycogen phosphorylase in complex with 52
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogen metabolism
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
2-(4-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsKyriakis, E. / Koulas, S.M. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ...Title: Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ex-vivo cellular experiments reveal novel potent inhibitors.
Authors: Chetter, B.A. / Kyriakis, E. / Barr, D. / Karra, A.G. / Katsidou, E. / Koulas, S.M. / Skamnaki, V.T. / Snape, T.J. / Psarra, A.G. / Leonidas, D.D. / Hayes, J.M.
History
DepositionFeb 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)97,7882
Polymers97,5191
Non-polymers2681
Water4,396244
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5754
Polymers195,0392
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4550 Å2
ΔGint-18 kcal/mol
Surface area56660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.957, 127.957, 115.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-O9T / 2-(4-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one


Mass: 268.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 49.44 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer, pH 6.7

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.5419 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 30, 2018
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.4→13.68 Å / Num. obs: 34314 / % possible obs: 91.2 % / Redundancy: 4.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3151 / CC1/2: 0.754 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→13.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.672 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21117 1679 4.9 %RANDOM
Rwork0.16823 ---
obs0.17035 32625 89.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.4→13.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6597 0 20 244 6861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0126767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.6379162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77221.576406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.344151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61559
X-RAY DIFFRACTIONr_chiral_restr0.0770.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025264
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5291.2813233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5881.9144036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6261.6093534
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.39717.0510215
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 114 -
Rwork0.264 2085 -
obs--78.9 %
Refinement TLS params.Method: refined / Origin x: 28.076 Å / Origin y: 21.174 Å / Origin z: 31.508 Å
111213212223313233
T0.0771 Å2-0.036 Å20.0044 Å2-0.111 Å2-0.0202 Å2--0.008 Å2
L0.5112 °20.0564 °20.0163 °2-0.46 °2-0.1464 °2--0.9009 °2
S-0.0253 Å °0.017 Å °0.0428 Å °-0.0041 Å °-0.0009 Å °0.0043 Å °0.0439 Å °-0.0729 Å °0.0262 Å °

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