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- PDB-2qln: Glycogen Phosphorylase b in complex with N-4-phenylbenzoyl-N'-bet... -

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Basic information

Entry
Database: PDB / ID: 2qln
TitleGlycogen Phosphorylase b in complex with N-4-phenylbenzoyl-N'-beta-D-glucopyranosyl urea
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate
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-F59 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsOikonomakos, N.G. / Chrysina, E.D. / Tiraidis, C. / Alexacou, K.-M. / Leonidas, D.D. / Sographos, S.E.
CitationJournal: To be Published
Title: N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation
Authors: Nagy, V. / Felf ldi, N. / Praly, J.-P. / Dosca, T. / Gergerly, P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M.N. / Alexacou, K.-M. / Konstantakaki, M.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 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)97,9222
Polymers97,5191
Non-polymers4021
Water4,882271
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,8434
Polymers195,0392
Non-polymers8052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.763, 128.763, 116.750
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: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-F59 / N-[(biphenyl-4-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine


Mass: 402.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 53808 / Num. obs: 53808 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 18.1
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 2632 / Rsym value: 0.367 / % possible all: 99.6

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Processing

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

2prj


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.201 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20947 2729 5.1 %RANDOM
Rwork0.18077 ---
obs0.18223 51023 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.805 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.169 Å0.215 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6613 0 29 271 6913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226792
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9589195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1875807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05723.524349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.041151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5281560
X-RAY DIFFRACTIONr_chiral_restr0.0760.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025213
X-RAY DIFFRACTIONr_nbd_refined0.1780.22807
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2342
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.26
X-RAY DIFFRACTIONr_mcbond_it0.5491.54187
X-RAY DIFFRACTIONr_mcangle_it0.9326515
X-RAY DIFFRACTIONr_scbond_it1.2133008
X-RAY DIFFRACTIONr_scangle_it1.9824.52680
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 205 -
Rwork0.198 3688 -
obs--99.59 %

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