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- PDB-6f3r: The crystal structure of Glycogen Phosphorylase in complex with 10c -

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Basic information

Entry
Database: PDB / ID: 6f3r
TitleThe crystal structure of Glycogen Phosphorylase in complex with 10c
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
Chem-CKZ / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsKyriakis, E. / Barkas, T.A. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: Eur J Med Chem / Year: 2018
Title: A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics ...Title: A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors.
Authors: Kun, S. / Begum, J. / Kyriakis, E. / Stamati, E.C.V. / Barkas, T.A. / Szennyes, E. / Bokor, E. / Szabo, K.E. / Stravodimos, G.A. / Sipos, A. / Docsa, T. / Gergely, P. / Moffatt, C. / ...Authors: Kun, S. / Begum, J. / Kyriakis, E. / Stamati, E.C.V. / Barkas, T.A. / Szennyes, E. / Bokor, E. / Szabo, K.E. / Stravodimos, G.A. / Sipos, A. / Docsa, T. / Gergely, P. / Moffatt, C. / Patraskaki, M.S. / Kokolaki, M.C. / Gkerdi, A. / Skamnaki, V.T. / Leonidas, D.D. / Somsak, L. / Hayes, J.M.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: 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
Item: _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)98,0653
Polymers97,4221
Non-polymers6432
Water4,468248
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1306
Polymers194,8452
Non-polymers1,2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5720 Å2
ΔGint-22 kcal/mol
Surface area56700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.874, 128.874, 116.431
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: 97422.398 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-CKZ / (2~{S},3~{R},4~{R},5~{S},6~{R})-2-[5-(9~{H}-fluoren-2-yl)-4~{H}-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,4,5-triol


Mass: 395.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 50.43 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→129 Å / Num. obs: 75805 / % possible obs: 98.1 % / Redundancy: 15.2 % / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 4.1 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 1.9→129 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 4.552 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16037 3718 4.9 %RANDOM
Rwork0.13274 ---
obs0.13411 72024 97.78 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.331 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-0 Å2-0 Å2
2--1.04 Å20 Å2
3----2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.9→129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 44 248 6881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196803
X-RAY DIFFRACTIONr_bond_other_d0.0020.026310
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9529218
X-RAY DIFFRACTIONr_angle_other_deg1.042.99614579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28323.506348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.233151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2381560
X-RAY DIFFRACTIONr_chiral_restr0.1150.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021468
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_it2.9032.3243243
X-RAY DIFFRACTIONr_mcbond_other2.9022.3223242
X-RAY DIFFRACTIONr_mcangle_it3.8043.4584050
X-RAY DIFFRACTIONr_mcangle_other3.8043.464051
X-RAY DIFFRACTIONr_scbond_it5.0642.9923560
X-RAY DIFFRACTIONr_scbond_other5.0632.9923561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4364.2375166
X-RAY DIFFRACTIONr_long_range_B_refined8.81227.8847549
X-RAY DIFFRACTIONr_long_range_B_other8.81127.8837550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 257 -
Rwork0.169 5204 -
obs--96.64 %
Refinement TLS params.Method: refined / Origin x: 28.323 Å / Origin y: 21.34 Å / Origin z: 31.639 Å
111213212223313233
T0.0344 Å2-0.043 Å20.0024 Å2-0.0726 Å2-0.03 Å2--0.0435 Å2
L0.6202 °20.0624 °20.0011 °2-0.5046 °2-0.1251 °2--0.9153 °2
S-0.0334 Å °0.0328 Å °0.0552 Å °-0.0213 Å °0.0005 Å °0.0194 Å °0.0657 Å °-0.0959 Å °0.033 Å °

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