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Basic information

Entry
Database: PDB / ID: 1ww3
TitleCrystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoroacetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / 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-(trifluoroacetyl)-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsAnagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Hadjiloi, T. / Tiraidis, C. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. ...Anagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Hadjiloi, T. / Tiraidis, C. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. / Gergely, P. / Kolisis, F.N. / Oikonomakos, N.G.
Citation
Journal: Bioorg.Med.Chem. / Year: 2006
Title: Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-d-glucopyranosylamine and N-trifluoroacetyl-beta-d-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase
Authors: Anagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Hadjiloi, T. / Tiraidis, C. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. / Gergely, P. / Kolisis, F.N. / Oikonomakos, N.G.
#1: Journal: Protein Sci. / Year: 1995
Title: N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose
Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R.
#2: 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.
History
DepositionDec 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8143
Polymers97,2911
Non-polymers5222
Water7,242402
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6276
Polymers194,5822
Non-polymers1,0454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6620 Å2
ΔGint-10 kcal/mol
Surface area57000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.789, 128.789, 116.234
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: 97291.203 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: Sugar ChemComp-NTF / N-(trifluoroacetyl)-beta-D-glucopyranosylamine / N-TRIFLURO-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE / N-(trifluoroacetyl)-beta-D-glucosylamine / N-(trifluoroacetyl)-D-glucosylamine / N-(trifluoroacetyl)-glucosylamine


Type: D-saccharide / Mass: 275.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H12F3NO6
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.43 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10mM Bes buffer, 3mM DDT, 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: Mar 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→28.07 Å / Num. obs: 568131 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4331 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PRJ

2prj


Resolution: 1.8→28.07 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3321583.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4511 5 %RANDOM
Rwork0.191 ---
obs0.191 89583 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.7074 Å2 / ksol: 0.364583 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å20 Å20 Å2
2--3.49 Å20 Å2
3----6.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 33 402 7015
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 707 4.9 %
Rwork0.279 13749 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.PARAMPLP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4NBF_NEW.PARAMNBF_NEW.TOP

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