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- PDB-6s52: The crystal structure of glycogen phosphorylase in complex with 14 -

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Basic information

Entry
Database: PDB / ID: 6s52
TitleThe crystal structure of glycogen phosphorylase in complex with 14
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / phosphorylase / inhibitor / C-beta-D-glucopyranosyl tetrazole
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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-KVN / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.37 Å
AuthorsKyriakis, E. / Solovou, T.G.A. / Papaioannou, O.S.E. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl ...Title: The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design.
Authors: Kyriakis, E. / Karra, A.G. / Papaioannou, O. / Solovou, T. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Szennyes, E. / Bokor, E. / Kun, S. / Psarra, A.G. / Somsak, L. / Leonidas, D.D.
History
DepositionJun 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9783
Polymers97,4221
Non-polymers5552
Water4,234235
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9566
Polymers194,8452
Non-polymers1,1114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5800 Å2
ΔGint-21 kcal/mol
Surface area56540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.128, 128.128, 115.823
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: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-KVN / (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(5-phenyl-1,2,3,4-tetrazol-2-yl)oxane-3,4,5-triol


Mass: 308.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


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


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
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 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.37→13.75 Å / Num. obs: 35891 / % possible obs: 91.1 % / Redundancy: 5.2 % / CC1/2: 0.995 / Rsym value: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3175 / CC1/2: 0.826 / Rsym value: 0.567 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.37→13.75 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.928 / SU B: 14.067 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20385 1795 5 %RANDOM
Rwork0.14563 ---
obs0.14858 34064 90.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 26.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.37→13.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 37 235 6861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176284
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6449174
X-RAY DIFFRACTIONr_angle_other_deg1.3791.57514518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2465807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18721.576406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6811559
X-RAY DIFFRACTIONr_chiral_restr0.0840.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021517
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_it2.1951.6033237
X-RAY DIFFRACTIONr_mcbond_other2.1941.6023236
X-RAY DIFFRACTIONr_mcangle_it3.3372.3964041
X-RAY DIFFRACTIONr_mcangle_other3.3362.3984042
X-RAY DIFFRACTIONr_scbond_it3.3722.0433539
X-RAY DIFFRACTIONr_scbond_other3.3722.0433540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2232.8965134
X-RAY DIFFRACTIONr_long_range_B_refined6.41518.4897515
X-RAY DIFFRACTIONr_long_range_B_other6.40518.4317486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.37→2.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 109 -
Rwork0.237 2106 -
obs--77.1 %
Refinement TLS params.Method: refined / Origin x: 28.171 Å / Origin y: 21.203 Å / Origin z: 31.489 Å
111213212223313233
T0.0256 Å2-0.0306 Å20.0051 Å2-0.047 Å2-0.0245 Å2--0.0357 Å2
L0.5872 °20.0188 °2-0.0216 °2-0.4469 °2-0.1199 °2--0.8475 °2
S-0.0274 Å °0.0156 Å °0.0424 Å °0.0025 Å °0.0017 Å °0.0075 Å °0.0477 Å °-0.0857 Å °0.0258 Å °

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