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- PDB-2qrg: Glycogen Phosphorylase b in complex with (1R)-3'-(4-methoxyphenyl... -

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Basic information

Entry
Database: PDB / ID: 2qrg
TitleGlycogen Phosphorylase b in complex with (1R)-3'-(4-methoxyphenyl)-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-M07 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsKizilis, 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 1.0Aug 5, 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 / 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 / _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)97,8452
Polymers97,5191
Non-polymers3251
Water6,702372
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6894
Polymers195,0392
Non-polymers6512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.816, 128.816, 116.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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-M07 / (5R,7R,8S,9S,10R)-7-(HYDROXYMETHYL)-3-(4-METHOXYPHENYL)-1,6-DIOXA-2-AZASPIRO[4.5]DEC-2-ENE-8,9,10-TRIOL / (1R)-3'-(4-METHOXYPHENYL)-SPIRO[1,5-ANHYDRO-D-GLUCITOL-1,5'-ISOXAZOLINE]


Mass: 325.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
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: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2006
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 82746 / Num. obs: 82746 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.056 / Net I/σ(I): 16.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.433 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2PRJ

2prj


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.625 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21097 4126 5 %RANDOM
Rwork0.1895 ---
obs0.19057 78563 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.119 Å0.133 Å
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 23 372 7004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226782
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9589183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0545807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04223.506348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.496151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8231560
X-RAY DIFFRACTIONr_chiral_restr0.0710.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025199
X-RAY DIFFRACTIONr_nbd_refined0.180.22861
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.23
X-RAY DIFFRACTIONr_mcbond_it0.5011.54175
X-RAY DIFFRACTIONr_mcangle_it0.85526512
X-RAY DIFFRACTIONr_scbond_it1.18632992
X-RAY DIFFRACTIONr_scangle_it1.9094.52671
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 312 -
Rwork0.241 5665 -
obs--98.24 %

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