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- PDB-2qrp: Glycogen Phosphorylase b in complex with (1R)-3'-(2-naphthyl)-spi... -

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Basic information

Entry
Database: PDB / ID: 2qrp
TitleGlycogen Phosphorylase b in complex with (1R)-3'-(2-naphthyl)-spiro[1,5-anhydro-D-glucitol-1,5'-isoxazoline]
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphorylation / Pyridoxal phosphate
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
Chem-S06 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.86 Å
AuthorsGizilis, G. / Alexacou, K.M. / Chrysina, E.D. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G.
CitationJournal: Bioorg.Med.Chem. / Year: 2009
Title: Glucose-based spiro-isoxazolines: a new family of potent glycogen phosphorylase inhibitors.
Authors: Benltifa, M. / Hayes, J.M. / Vidal, S. / Gueyrard, D. / Goekjian, P.G. / Praly, J.P. / Kizilis, G. / Tiraidis, C. / Alexacou, K.M. / Chrysina, E.D. / Zographos, S.E. / Leonidas, D.D. / ...Authors: Benltifa, M. / Hayes, J.M. / Vidal, S. / Gueyrard, D. / Goekjian, P.G. / Praly, J.P. / Kizilis, G. / Tiraidis, C. / Alexacou, K.M. / Chrysina, E.D. / Zographos, S.E. / Leonidas, D.D. / Archontis, G. / Oikonomakos, N.G.
History
DepositionJul 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)99,03917
Polymers97,5191
Non-polymers1,51916
Water15,655869
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,07734
Polymers195,0392
Non-polymers3,03932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)126.020, 126.020, 114.881
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-1274-

HOH

21A-1677-

HOH

31A-1743-

HOH

DetailsDimeric glycogen phosphorylase is the physiologiacally active species. The second part of the biological assembly is generated by the two fold axis: y,x,1-z

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-S06 / (3S,5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(2-naphthyl)-1,6-dioxa-2-azaspiro[4.5]decane-8,9,10-triol / (1R)-3'-(2-naphthyl)-spiro[1,5-anhydro-D-glucitol-1,5'-isoxazoline]


Mass: 347.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21NO6
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8073 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2006
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8073 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. all: 77891 / Num. obs: 77891 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 22.3
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.344 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 1.86→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.89 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21919 3916 5 %RANDOM
Rwork0.19356 ---
obs0.19487 73897 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.133 Å0.153 Å
Refinement stepCycle: LAST / Resolution: 1.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 85 869 7578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226846
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.9639251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2255808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22623.467349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.624151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5291561
X-RAY DIFFRACTIONr_chiral_restr0.0680.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025210
X-RAY DIFFRACTIONr_nbd_refined0.1820.23580
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2854
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.240
X-RAY DIFFRACTIONr_mcbond_it0.4191.54197
X-RAY DIFFRACTIONr_mcangle_it0.71926550
X-RAY DIFFRACTIONr_scbond_it0.9933042
X-RAY DIFFRACTIONr_scangle_it1.5854.52700
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 282 -
Rwork0.232 5358 -
obs-5358 99.68 %

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