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- PDB-3mrv: Glycogen phosphorylase complexed with 3-hydroxybenzaldehyde-4-(be... -

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Basic information

Entry
Database: PDB / ID: 3mrv
TitleGlycogen phosphorylase complexed with 3-hydroxybenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Glycogenolysis / type 2 diabetes / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-16F / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsAlexacou, K.-M.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors
Authors: Alexacou, K.M. / Tenchiu Deleanu, A.C. / Chrysina, E.D. / Charavgi, M.D. / Kostas, I.D. / Zographos, S.E. / Oikonomakos, N.G. / Leonidas, D.D.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / software / struct_conn
Item: _software.classification / _software.name / _software.version
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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 1.5Nov 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)98,3124
Polymers97,5191
Non-polymers7933
Water4,414245
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6248
Polymers195,0392
Non-polymers1,5866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5130 Å2
ΔGint-17 kcal/mol
Surface area56690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.866, 128.866, 116.324
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: Sugar ChemComp-16F / N-({(2Z)-2-[(3-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine / 3-hydroxybenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone / N-({(2Z)-2-[(3-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucosylamine / N-({(2Z)-2-[(3-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-D-glucosylamine / N-({(2Z)-2-[(3-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-glucosylamine


Type: D-saccharide / Mass: 357.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N3O6S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 50.32 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 20mM inhibitor in 20% DMSO soaked with T-state native enzyme crystals for 3.5 hrs, pH 6.7, SMALL TUBES, temperature 289K

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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 19, 2007
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04498 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 72392 / Num. obs: 72392 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.73
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 1.94→29.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.303 / SU ML: 0.096 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21633 3643 5 %RANDOM
Rwork0.19226 ---
obs0.1935 68577 99.24 %-
all-68578 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.636 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.94→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 52 245 6901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.969245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70823.543350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.436151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0551559
X-RAY DIFFRACTIONr_chiral_restr0.0880.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215237
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.22828
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24614
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6591.54041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27726528
X-RAY DIFFRACTIONr_scbond_it1.92832786
X-RAY DIFFRACTIONr_scangle_it3.2794.52715
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 255 -
Rwork0.249 5023 -
obs--99.96 %

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