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- PDB-5ox3: Glycogen Phosphorylase in complex with SzB102v -

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Basic information

Entry
Database: PDB / ID: 5ox3
TitleGlycogen Phosphorylase in complex with SzB102v
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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-B1N / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)98,3414
Polymers97,4221
Non-polymers9193
Water4,828268
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6828
Polymers194,8452
Non-polymers1,8376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7090 Å2
ΔGint-28 kcal/mol
Surface area56750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.550, 128.550, 116.190
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: Sugar ChemComp-B1N / (1S)-1,5-anhydro-1-[3-(4-hydroxyphenyl)-1H-1,2,4-triazol-5-yl]-D-glucitol / (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[3-(4-hydroxyphenyl)-1~{H}-1,2,4-triazol-5-yl]oxane-3,4,5-triol


Type: D-saccharide / Mass: 323.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O6
#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.: 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: 2.46 Å3/Da / Density % sol: 50.07 %
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: 1.9→38.4 Å / Num. obs: 72951 / % possible obs: 95.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10736 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→38.4 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.191 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16261 3664 5 %RANDOM
Rwork0.13386 ---
obs0.13531 69283 94.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 33.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0 Å2
2--0.27 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 61 268 6919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196807
X-RAY DIFFRACTIONr_bond_other_d0.0020.026486
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9629223
X-RAY DIFFRACTIONr_angle_other_deg0.9483.00114855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91723.545347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.008151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8941559
X-RAY DIFFRACTIONr_chiral_restr0.0840.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021654
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_it2.5091.683239
X-RAY DIFFRACTIONr_mcbond_other2.5061.6783238
X-RAY DIFFRACTIONr_mcangle_it3.6122.54044
X-RAY DIFFRACTIONr_mcangle_other3.6152.5024045
X-RAY DIFFRACTIONr_scbond_it4.6412.3673568
X-RAY DIFFRACTIONr_scbond_other4.6042.3593564
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other73.3125173
X-RAY DIFFRACTIONr_long_range_B_refined8.54220.387497
X-RAY DIFFRACTIONr_long_range_B_other8.54520.3977498
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
Rfree0.257 262 -
Rwork0.224 5172 -
obs--96.67 %
Refinement TLS params.Method: refined / Origin x: 28.268 Å / Origin y: 21.323 Å / Origin z: 31.609 Å
111213212223313233
T0.0504 Å2-0.0419 Å20.005 Å2-0.0953 Å2-0.0264 Å2--0.0143 Å2
L0.6008 °20.0717 °2-0.0334 °2-0.4893 °2-0.1297 °2--0.933 °2
S-0.033 Å °0.0474 Å °0.0454 Å °-0.0228 Å °0.0035 Å °0.0132 Å °0.0675 Å °-0.0969 Å °0.0295 Å °

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