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- PDB-2ffr: Crystallographic studies on N-azido-beta-D-glucopyranosylamine, a... -

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Basic information

Entry
Database: PDB / ID: 2ffr
TitleCrystallographic studies on N-azido-beta-D-glucopyranosylamine, an inhibitor of glycogen phosphorylase: comparison with N-acetyl-beta-D-glucopyranosylamine
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / inhibition / type 2 diabetes
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
N-(azidoacetyl)-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsPetsalakis, E.I. / Chrysina, E.D. / Tiraidis, C. / Hadjiloi, T. / Leonidas, D.D. / Oikonomakos, N.G. / Aich, U. / Varghese, B. / Loganathan, D.
Citation
Journal: Bioorg.Med.Chem. / Year: 2006
Title: Crystallographic studies on N-azidoacetyl-beta-d-glucopyranosylamine, an inhibitor of glycogen phosphorylase: Comparison with N-acetyl-beta-d-glucopyranosylamine.
Authors: Petsalakis, E.I. / Chrysina, E.D. / Tiraidis, C. / Hadjiloi, T. / Leonidas, D.D. / Oikonomakos, N.G. / Aich, U. / Varghese, B. / Loganathan, D.
#1: Journal: Bioorg.Med.Chem. / Year: 2006
Title: Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoracetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase
Authors: Anagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Tiraidis, C. / Hadjiloi, T. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. / Gergely, P. / Kolisis, F.N. / Oikonomakos, N.G.
History
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 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

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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)95,7903
Polymers95,2811
Non-polymers5092
Water6,449358
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,5816
Polymers190,5622
Non-polymers1,0194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6650 Å2
ΔGint-14 kcal/mol
Surface area56390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.626, 128.626, 116.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimeric glycogen phosphorylase is the physiologiacally active species

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 95280.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Sugar ChemComp-DL6 / N-(azidoacetyl)-beta-D-glucopyranosylamine / 2-AZIDO-N-((2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)ACETAMIDE / N-AZIDOACETYL-BETA-D-GLUCOPYRANOSYLAMINE / N-(azidoacetyl)-beta-D-glucosylamine / N-(azidoacetyl)-D-glucosylamine / N-(azidoacetyl)-glucosylamine


Type: D-saccharide / Mass: 262.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes buffer, 0.1 mM EDTA, 0.02% NaN3, 3 mM DTT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.03→29.48 Å / Num. all: 63405 / Num. obs: 62829 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.8
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 3088 / Rsym value: 0.563 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1WW2

1ww2


Resolution: 2.03→29.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3632333.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3172 5.1 %RANDOM
Rwork0.184 ---
obs0.184 62790 99.1 %-
all-63405 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1025 Å2 / ksol: 0.311173 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å20 Å20 Å2
2--3.31 Å20 Å2
3----6.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.03→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 33 358 6981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 517 5 %
Rwork0.235 9726 -
obs-63405 98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3plp.paramplp.top
X-RAY DIFFRACTION4dl6.pardl6.top

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