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- PDB-4yi5: Crystal structure of Gpb in complex with 4b -

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Basic information

Entry
Database: PDB / ID: 4yi5
TitleCrystal structure of Gpb in complex with 4b
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-4D1 / 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.
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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)98,4124
Polymers97,4221
Non-polymers9903
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-4 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.540, 128.540, 116.630
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-4D1 / N-({(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}carbamoyl)-beta-D-glucopyranosylamine


Mass: 394.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N2O7
#4: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 52.23 %
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 4, 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→38.88 Å / Num. obs: 12263 / % possible obs: 91.5 % / Redundancy: 2.8 % / Rsym value: 0.13 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.8 / % possible all: 94.6

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Processing

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

4mho


Resolution: 1.8→38.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.708 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23042 4005 4.9 %RANDOM
Rwork0.19388 ---
obs0.1957 77765 90.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-0 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 66 384 7033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196804
X-RAY DIFFRACTIONr_bond_other_d0.0020.026489
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9629217
X-RAY DIFFRACTIONr_angle_other_deg0.9743.00214861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43223.545347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.139151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1361559
X-RAY DIFFRACTIONr_chiral_restr0.0830.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021656
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_it1.6293.0383235
X-RAY DIFFRACTIONr_mcbond_other1.6283.0363234
X-RAY DIFFRACTIONr_mcangle_it2.5554.5474039
X-RAY DIFFRACTIONr_mcangle_other2.5554.5484040
X-RAY DIFFRACTIONr_scbond_it2.1433.4273569
X-RAY DIFFRACTIONr_scbond_other2.1413.4233565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4865.0165172
X-RAY DIFFRACTIONr_long_range_B_refined5.27624.9297840
X-RAY DIFFRACTIONr_long_range_B_other5.27624.9367841
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
Rfree0.296 282 -
Rwork0.261 5951 -
obs--93.94 %

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