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- PDB-6s4o: The crystal structure of glycogen phosphorylase in complex with 9 -

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Basic information

Entry
Database: PDB / ID: 6s4o
TitleThe crystal structure of glycogen phosphorylase in complex with 9
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / phosphorylase / inhibitor / C-beta-D-glucopyranosyl imidazole
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
INOSINIC ACID / Chem-KV5 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.35 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 28, 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

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3744
Polymers97,4221
Non-polymers9523
Water4,396244
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,7488
Polymers194,8452
Non-polymers1,9036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6840 Å2
ΔGint-33 kcal/mol
Surface area55980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.207, 128.207, 115.941
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-1241-

HOH

21A-1244-

HOH

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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-KV5 / (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-naphthalen-2-yl-1~{H}-imidazol-4-yl)oxane-3,4,5-triol


Mass: 356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: 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

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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: 2.55 Å3/Da / Density % sol: 51.75 %
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: 2.35→13.7 Å / Num. obs: 37798 / % possible obs: 93.2 % / Redundancy: 5.3 % / CC1/2: 0.994 / Rsym value: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3389 / CC1/2: 0.907 / Rsym value: 0.456 / % possible all: 80.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→13.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.168 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20741 1839 4.9 %RANDOM
Rwork0.15266 ---
obs0.15528 35896 92.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 26.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.35→13.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 64 244 6890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136799
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176291
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6459210
X-RAY DIFFRACTIONr_angle_other_deg1.2771.57514535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71721.576406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.577151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3241559
X-RAY DIFFRACTIONr_chiral_restr0.0710.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021523
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_it1.7251.6723233
X-RAY DIFFRACTIONr_mcbond_other1.7221.6713232
X-RAY DIFFRACTIONr_mcangle_it2.7292.5024036
X-RAY DIFFRACTIONr_mcangle_other2.7292.5034037
X-RAY DIFFRACTIONr_scbond_it2.8192.0953566
X-RAY DIFFRACTIONr_scbond_other2.8192.0943566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4762.9985175
X-RAY DIFFRACTIONr_long_range_B_refined5.85919.3927512
X-RAY DIFFRACTIONr_long_range_B_other5.85619.3387488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 96 -
Rwork0.236 2248 -
obs--79.08 %
Refinement TLS params.Method: refined / Origin x: 28.158 Å / Origin y: 21.271 Å / Origin z: 31.498 Å
111213212223313233
T0.0252 Å2-0.0317 Å20.0042 Å2-0.0515 Å2-0.0212 Å2--0.0245 Å2
L0.5629 °20.0379 °2-0.0291 °2-0.4193 °2-0.1015 °2--0.8313 °2
S-0.0335 Å °0.0257 Å °0.0455 Å °-0.0061 Å °0.0045 Å °0.0155 Å °0.0549 Å °-0.0817 Å °0.029 Å °

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