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- PDB-3g2h: Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,... -

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Basic information

Entry
Database: PDB / ID: 3g2h
TitleCrystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / Glycogen phosphorylase / amide-1 / 2 / 3-triazole bioisosterism / 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
INOSINIC ACID / Chem-KOT / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChrysina, E.D. / Bokor, E. / Alexacou, K.-M. / Charavgi, M.-D. / Oikonomakos, G.N. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G. / Somsak, L.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection.
Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Cruciani, G. / Son, J.C. / Bichard, C.J. / Fleet, G.W. / Oikonomakos, N.G. / Kontou, M. / Zographos, S.E.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: 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 1.3Sep 6, 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 22, 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)98,2534
Polymers97,5191
Non-polymers7343
Water3,891216
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)196,5068
Polymers195,0392
Non-polymers1,4676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4370 Å2
ΔGint-18.1 kcal/mol
Surface area55490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.287, 127.287, 115.615
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-KOT / 1-beta-D-glucopyranosyl-4-phenyl-1H-1,2,3-triazole / 1-beta-D-glucosyl-4-phenyl-1H-1,2,3-triazole / 1-D-glucosyl-4-phenyl-1H-1,2,3-triazole / 1-glucosyl-4-phenyl-1H-1,2,3-triazole


Type: D-saccharide / Mass: 307.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: pH 6.8, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 60007 / % possible obs: 96.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.5
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2991 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PRJ

2prj


Resolution: 2.03→29.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.784 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22019 3049 5.1 %RANDOM
Rwork0.19572 ---
obs0.19697 56675 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.272 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.03→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6576 0 49 216 6841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226776
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9639177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77123.536345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.277151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6141559
X-RAY DIFFRACTIONr_chiral_restr0.0730.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025186
X-RAY DIFFRACTIONr_nbd_refined0.1890.23319
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2428
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.27
X-RAY DIFFRACTIONr_mcbond_it0.5411.54125
X-RAY DIFFRACTIONr_mcangle_it0.94926489
X-RAY DIFFRACTIONr_scbond_it1.27233003
X-RAY DIFFRACTIONr_scangle_it2.0844.52688
LS refinement shellResolution: 2.03→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 203 -
Rwork0.252 4203 -
obs--98.44 %

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