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- PDB-5ox1: Glycogen Phosphorylase in complex with JLH270 -

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Basic information

Entry
Database: PDB / ID: 5ox1
TitleGlycogen Phosphorylase in complex with JLH270
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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-B1K / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsKyriakis, E. / Stravodimos, G.A. / Kantsadi, A.L. / Chatzileontiadou, D.S.M. / Leonidas, D.D.
CitationJournal: Bioorg. Chem. / Year: 2018
Title: Probing the beta-pocket of the active site of human liver glycogen phosphorylase with 3-(C-beta-d-glucopyranosyl)-5-(4-substituted-phenyl)-1, 2, 4-triazole inhibitors.
Authors: Kyriakis, E. / Solovou, T.G.A. / Kun, S. / Czifrak, K. / Szocs, B. / Juhasz, L. / Bokor, E. / Stravodimos, G.A. / Kantsadi, A.L. / Chatzileontiadou, D.S.M. / Skamnaki, V.T. / Somsak, L. / Leonidas, D.D.
History
DepositionSep 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release

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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)98,0854
Polymers97,4221
Non-polymers6633
Water4,828268
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1708
Polymers194,8452
Non-polymers1,3256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6300 Å2
ΔGint-15 kcal/mol
Surface area56720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.660, 128.660, 116.210
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-B1K / (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methoxyphenyl)-1~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol / JLH270


Mass: 337.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N3O6
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0403 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 1.85→38.4 Å / Num. obs: 80695 / % possible obs: 97.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 11707 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→38.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.887 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16944 3962 4.9 %RANDOM
Rwork0.141 ---
obs0.14242 76693 96.69 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 33.072 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å2-0 Å2
2--0.29 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.85→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 43 268 6901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196790
X-RAY DIFFRACTIONr_bond_other_d0.0020.026489
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9589195
X-RAY DIFFRACTIONr_angle_other_deg0.9523.00114859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12223.545347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.667151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191559
X-RAY DIFFRACTIONr_chiral_restr0.0840.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021652
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_it1.6961.7963241
X-RAY DIFFRACTIONr_mcbond_other1.6941.7953240
X-RAY DIFFRACTIONr_mcangle_it2.6432.6794046
X-RAY DIFFRACTIONr_mcangle_other2.6432.684047
X-RAY DIFFRACTIONr_scbond_it2.9232.2893549
X-RAY DIFFRACTIONr_scbond_other2.9232.2913550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7353.2675148
X-RAY DIFFRACTIONr_long_range_B_refined6.38621.1947469
X-RAY DIFFRACTIONr_long_range_B_other6.38621.217470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 319 -
Rwork0.236 5606 -
obs--97.12 %
Refinement TLS params.Method: refined / Origin x: 28.275 Å / Origin y: 21.324 Å / Origin z: 31.61 Å
111213212223313233
T0.0555 Å2-0.0384 Å20.0032 Å2-0.0952 Å2-0.0265 Å2--0.0144 Å2
L0.6067 °20.0701 °2-0.0267 °2-0.4755 °2-0.1377 °2--0.8893 °2
S-0.0345 Å °0.0412 Å °0.0477 Å °-0.0184 Å °0.0032 Å °0.0124 Å °0.063 Å °-0.088 Å °0.0313 Å °

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