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- PDB-2qn3: Glycogen Phosphorylase in complex with N-4-chlorobenzoyl-N-beta-D... -

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Basic information

Entry
Database: PDB / ID: 2qn3
TitleGlycogen Phosphorylase in complex with N-4-chlorobenzoyl-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 / 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-F55 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 Å
AuthorsChrysina, E.D. / Tiraidis, C. / Alexacou, K.-M. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G.
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 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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)97,8802
Polymers97,5191
Non-polymers3611
Water5,981332
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7604
Polymers195,0392
Non-polymers7212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.841, 128.841, 116.486
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: Sugar ChemComp-F55 / N-{[(4-chlorophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine / N-{[(4-chlorophenyl)carbonyl]carbamoyl}-beta-D-glucosylamine / N-{[(4-chlorophenyl)carbonyl]carbamoyl}-D-glucosylamine / N-{[(4-chlorophenyl)carbonyl]carbamoyl}-glucosylamine


Type: D-saccharide / Mass: 360.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17ClN2O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 50.37 %
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: SRS / Beamline: PX9.6 / Wavelength: 0.912 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.95→99 Å / Num. all: 70275 / Num. obs: 70275 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.046 / Net I/σ(I): 20.1
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 3280 / Rsym value: 0.318 / % possible all: 93.1

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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: 1.96→91.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.179 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 3563 5.1 %RANDOM
Rwork0.18469 ---
obs0.1858 66980 99.82 %-
all-66980 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.133 Å0.156 Å
Refinement stepCycle: LAST / Resolution: 1.96→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 24 332 6988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226805
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9579213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0965810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11923.543350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.679151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5621560
X-RAY DIFFRACTIONr_chiral_restr0.0730.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025222
X-RAY DIFFRACTIONr_nbd_refined0.1750.22807
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2350
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.26
X-RAY DIFFRACTIONr_mcbond_it0.5361.54199
X-RAY DIFFRACTIONr_mcangle_it0.90126537
X-RAY DIFFRACTIONr_scbond_it1.20533007
X-RAY DIFFRACTIONr_scangle_it1.9314.52676
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 235 -
Rwork0.23 4864 -
obs--99.69 %

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