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- PDB-4eky: Crystal structure of GPb in complex with DK15 -

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Basic information

Entry
Database: PDB / ID: 4eky
TitleCrystal structure of GPb in complex with DK15
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha/beta protein
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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-D1J / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsKantsadi, A.L. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: Eur.J.Med.Chem. / Year: 2012
Title: The binding of C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides to glycogen phosphorylase b: Synthesis, biochemical and biological assessment.
Authors: Kantsadi, A.L. / Manta, S. / Psarra, A.M. / Dimopoulou, A. / Kiritsis, C. / Parmenopoulou, V. / Skamnaki, V.T. / Zoumpoulakis, P. / Zographos, S.E. / Leonidas, D.D. / Komiotis, D.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 1.4Dec 6, 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)95,8492
Polymers95,5091
Non-polymers3401
Water2,684149
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,6994
Polymers191,0182
Non-polymers6812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4600 Å2
ΔGint-20 kcal/mol
Surface area57530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.674, 128.674, 116.564
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: 95509.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-D1J / 1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione


Mass: 340.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5419 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 7, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.45→13.7 Å / Num. all: 33602 / Num. obs: 33602 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.109 / Net I/σ(I): 13.8
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4314 / Rsym value: 0.491 / % possible all: 82.4

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Processing

Software
NameClassification
CrysalisProdata collection
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3SYM
Resolution: 2.45→13.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.722 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23038 1700 5.1 %RANDOM
Rwork0.16088 ---
obs0.16435 31848 92.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.45→13.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 24 149 6777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9579188
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08723.534348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.638151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.991559
X-RAY DIFFRACTIONr_chiral_restr0.1250.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215200
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9321.54035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81326517
X-RAY DIFFRACTIONr_scbond_it2.94432751
X-RAY DIFFRACTIONr_scangle_it4.9574.52671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 125 -
Rwork0.241 1962 -
obs--81.02 %

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