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- PDB-2iei: Crystal structure of rabbit muscle glycogen phosphorylase in comp... -

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Basic information

Entry
Database: PDB / ID: 2iei
TitleCrystal structure of rabbit muscle glycogen phosphorylase in complex with 3,4-dihydro-2-quinolone
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / DIABETES / GLUCOSE
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-FRX / Chem-PLR / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBirch, A.M. / Kenny, P.W. / Oikonomakos, N.G. / Otterbein, L. / Schofield, P. / Whittamore, P.R.O. / Whalley, D.P. / Rowsell, S. / Pauptit, R. / Pannifer, A. ...Birch, A.M. / Kenny, P.W. / Oikonomakos, N.G. / Otterbein, L. / Schofield, P. / Whittamore, P.R.O. / Whalley, D.P. / Rowsell, S. / Pauptit, R. / Pannifer, A. / Breed, J. / Minshull, C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Development of potent, orally active 1-substituted-3,4-dihydro-2-quinolone glycogen phosphorylase inhibitors.
Authors: Birch, A.M. / Kenny, P.W. / Oikonomakos, N.G. / Otterbein, L. / Schofield, P. / Whittamore, P.R. / Whalley, D.P.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9436
Polymers194,5822
Non-polymers1,3604
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-38 kcal/mol
Surface area54760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.402, 125.344, 129.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 97291.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-FRX / (S)-2-CHLORO-N-(1-(2-(2-HYDROXYETHYLAMINO)-2-OXOETHYL)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL)-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE


Mass: 446.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19ClN4O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.7
Details: 10mM BES, 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.002
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2002 / Details: Rh coated Si mirror
RadiationMonochromator: single crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 1.91→33 Å / Num. all: 109793 / Num. obs: 109793 / % possible obs: 80.52 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→33 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.856 / SU B: 5.284 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29742 5805 5 %RANDOM
Rwork0.25533 ---
obs0.25743 109793 80.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.185 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20 Å20 Å2
2--0.96 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.91→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12829 0 90 617 13536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.95817891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27751579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67123.551659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.823152257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.50115109
X-RAY DIFFRACTIONr_chiral_restr0.0720.21941
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210129
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.26388
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.28921
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2808
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3991.58173
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.678212746
X-RAY DIFFRACTIONr_scbond_it0.93235761
X-RAY DIFFRACTIONr_scangle_it1.4294.55145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 143 -
Rwork0.328 3210 -
obs--33.55 %

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