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- PDB-4mic: Crystal structure of Gpb in complex with SUGAR (N-{(2E)-3-[4-(PRO... -

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Basic information

Entry
Database: PDB / ID: 4mic
TitleCrystal structure of Gpb in complex with SUGAR (N-{(2E)-3-[4-(PROPAN-2-YL)PHENYL]PROP-2-ENOYL}-BETA-D-GLUCOPYRANOSYLAMINE) (S6)
ComponentsGlycogen phosphorylase, muscle form
Keywordstransferase/transferase inhibitor / alpha and beta protein / 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-26Y / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsKantsadi, A.L. / Chatzileontiadou, D.S.M. / Leonidas, D.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines.
Authors: Parmenopoulou, V. / Kantsadi, A.L. / Tsirkone, V.G. / Chatzileontiadou, D.S. / Manta, S. / Zographos, S.E. / Molfeta, C. / Archontis, G. / Agius, L. / Hayes, J.M. / Leonidas, D.D. / Komiotis, D.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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 1.5Dec 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)95,8602
Polymers95,5091
Non-polymers3511
Water2,036113
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7214
Polymers191,0182
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4400 Å2
ΔGint-20 kcal/mol
Surface area57230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.740, 128.740, 116.710
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 / Details: muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-26Y / N-{(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}-beta-D-glucopyranosylamine


Type: saccharide / Mass: 351.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C18H25NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM 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: Feb 22, 2013
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.45→18.23 Å / Num. all: 33056 / Num. obs: 33056 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.099 / Net I/σ(I): 6.3
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4997 / Rsym value: 0.531 / % possible all: 95.6

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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

3sym


Resolution: 2.45→18.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.792 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.596 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23354 1646 5 %RANDOM
Rwork0.18663 ---
obs0.18899 31316 89.96 %-
all-31316 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å20 Å2
2--0.72 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.45→18.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 25 113 6715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196767
X-RAY DIFFRACTIONr_bond_other_d0.0010.026466
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.9579163
X-RAY DIFFRACTIONr_angle_other_deg0.743.00114810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3935806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86823.545347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.392151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81559
X-RAY DIFFRACTIONr_chiral_restr0.0570.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021648
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 135 -
Rwork0.256 2400 -
obs--95.01 %

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