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- PDB-3cuw: Crystal structure of glycogen phosphorylase b in complex with N-(... -

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Basic information

Entry
Database: PDB / ID: 3cuw
TitleCrystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)oxamides
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogen phosphorylase / catalytic site / rational inhibitor design / 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-445 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsKyritsi, C. / Chrysina, E.D. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: To be Published
Title: Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides
Authors: Czifrak, K. / Kyritsi, C. / Felfoldi, N. / Dosca, T. / Gergely, P. / Chrysina, E.D. / Siafaka-Kapadai, A. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
History
DepositionApr 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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:
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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1723
Polymers97,5191
Non-polymers6532
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3446
Polymers195,0392
Non-polymers1,3054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5370 Å2
ΔGint-28.2 kcal/mol
Surface area56020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.418, 128.418, 116.353
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 / Details: muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-445 / N-[oxo(phenylamino)acetyl]-beta-D-glucopyranosylamine / N-[oxo(phenylamino)acetyl]-beta-D-glucosylamine / N-[oxo(phenylamino)acetyl]-D-glucosylamine / N-[oxo(phenylamino)acetyl]-glucosylamine


Type: D-saccharide / Mass: 326.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N2O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 287 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH6.7, SMALL TUBES, temperature 287K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 65843 / Num. obs: 65843 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.465 / % possible all: 99.4

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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 1HLF

1hlf


Resolution: 2→21.26 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.435 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21649 3338 5.1 %RANDOM
Rwork0.19156 ---
obs0.19282 62455 99.5 %-
all-65793 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2→21.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6637 0 46 255 6938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226834
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9619252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07623.533351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3711560
X-RAY DIFFRACTIONr_chiral_restr0.0730.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025242
X-RAY DIFFRACTIONr_nbd_refined0.1820.23007
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2351
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.26
X-RAY DIFFRACTIONr_mcbond_it0.5521.54191
X-RAY DIFFRACTIONr_mcangle_it0.94326538
X-RAY DIFFRACTIONr_scbond_it1.21833039
X-RAY DIFFRACTIONr_scangle_it1.9584.52714
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 226 -
Rwork0.233 4527 -
obs--98.96 %

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