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

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Basic information

Entry
Database: PDB / ID: 3cut
TitleCrystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)oxamide
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-179 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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 1.2Nov 1, 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)97,8962
Polymers97,5191
Non-polymers3761
Water2,918162
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)195,7914
Polymers195,0392
Non-polymers7532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4930 Å2
ΔGint-22.8 kcal/mol
Surface area56830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.712, 128.712, 116.819
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: Chemical ChemComp-179 / N-[(naphthalen-2-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine


Mass: 376.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 50.42 %
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: SRS / Beamline: PX10.1 / Wavelength: 1.04498 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2007
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04498 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 43315 / Num. obs: 43315 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 39.1 Å2 / Rsym value: 0.116 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.497 / % possible all: 99

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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: 2.3→29.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.039 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22028 2174 5 %RANDOM
Rwork0.19292 ---
obs0.19433 41102 98 %-
all-43276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.561 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2--1.11 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6637 0 27 162 6826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226815
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9579227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98923.533351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.956151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4571560
X-RAY DIFFRACTIONr_chiral_restr0.0780.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025231
X-RAY DIFFRACTIONr_nbd_refined0.1850.22877
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2303
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.22
X-RAY DIFFRACTIONr_mcbond_it0.6231.54180
X-RAY DIFFRACTIONr_mcangle_it1.08926538
X-RAY DIFFRACTIONr_scbond_it1.36533027
X-RAY DIFFRACTIONr_scangle_it2.2674.52689
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 158 -
Rwork0.249 2987 -
obs--99.06 %

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