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- PDB-4yi3: Crystal structure of Gpb in complex with 4a -

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Basic information

Entry
Database: PDB / ID: 4yi3
TitleCrystal structure of Gpb in complex with 4a
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein
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-4D0 / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKantsadi, A.L. / Chatzileontiadou, D.S.M. / Stravodimos, G.A. / Leonidas, D.D.
Funding support Greece, 1items
OrganizationGrant numberCountry
ARISTEIA" Action of the "Operational Programme Education and Lifelong Learning1492 Greece
CitationJournal: Curr Top Med Chem / Year: 2015
Title: Glycogen phosphorylase as a target for type 2 diabetes: synthetic, biochemical, structural and computational evaluation of novel N-acyl-N -( beta-D-glucopyranosyl) urea inhibitors.
Authors: Kantsadi, A.L. / Parmenopoulou, V. / Bakalov, D.N. / Snelgrove, L. / Stravodimos, G.A. / Chatzileontiadou, D.S. / Manta, S. / Panagiotopoulou, A. / Hayes, J.M. / Komiotis, D. / Leonidas, D.D.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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)98,5265
Polymers97,4221
Non-polymers1,1044
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-0 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.460, 128.460, 116.580
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-1344-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H10NO6P
#3: Chemical ChemComp-4D0 / N-{[3-(biphenyl-4-yl)propanoyl]carbamoyl}-beta-D-glucopyranosylamine


Mass: 430.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N2O7
#4: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM 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: Dec 3, 2014
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 1.8→38.36 Å / Num. all: 90140 / Num. obs: 6609 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rsym value: 0.078 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALAdata scaling
DENZOdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHO

4mho


Resolution: 1.8→38.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.348 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19762 4420 4.9 %RANDOM
Rwork0.1743 ---
obs0.17546 85720 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å2-0 Å2-0 Å2
2--0.76 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 73 346 6975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9639201
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18323.526346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.482151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2351559
X-RAY DIFFRACTIONr_chiral_restr0.0930.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215208
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.342.7133225
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1864.0594027
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0753.1053567
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.52123.51210333
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 303 -
Rwork0.256 6306 -
obs--99.91 %

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