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- PDB-4mi6: Crystal structure of Gpb in complex with SUGAR (N-[4-(5,6,7,8-TET... -

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Basic information

Entry
Database: PDB / ID: 4mi6
TitleCrystal structure of Gpb in complex with SUGAR (N-[4-(5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)BUTANOYL]-BETA-D-GLUCOPYRANOSYLAMINE)
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-26V / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKantsadi, L.A. / Chatzileontiadou, S.M.D. / 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 1.2Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Sep 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 1.4Dec 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)95,8882
Polymers95,5091
Non-polymers3791
Water4,774265
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7774
Polymers191,0182
Non-polymers7592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4600 Å2
ΔGint-23 kcal/mol
Surface area57110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.900, 128.900, 116.540
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 / Fragment: unp residues 13-837 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Strain: M / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-26V / N-[4-(5,6,7,8-tetrahydronaphthalen-2-yl)butanoyl]-beta-D-glucopyranosylamine


Type: saccharide / Mass: 379.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H29NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
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: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2013
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→23.94 Å / Num. all: 75897 / Num. obs: 75897 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.055 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 10836 / Rsym value: 0.365 / % possible all: 97.1

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Processing

Software
NameClassification
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3SYM

3sym


Resolution: 1.9→23.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.725 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 3821 5 %RANDOM
Rwork0.16131 ---
obs0.16265 72040 97.78 %-
all-72040 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.341 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å20 Å2
2--0.71 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 27 265 6893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196801
X-RAY DIFFRACTIONr_bond_other_d0.0020.026501
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9579211
X-RAY DIFFRACTIONr_angle_other_deg0.8043.00214895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31623.571350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9721559
X-RAY DIFFRACTIONr_chiral_restr0.0730.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021657
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_it1.522.8963241
X-RAY DIFFRACTIONr_mcbond_other1.522.8953240
X-RAY DIFFRACTIONr_mcangle_it2.4614.3324047
X-RAY DIFFRACTIONr_mcangle_other2.4614.3344048
X-RAY DIFFRACTIONr_scbond_it2.1193.2693560
X-RAY DIFFRACTIONr_scbond_other2.1193.2693560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5774.7755163
X-RAY DIFFRACTIONr_long_range_B_refined5.18223.3097696
X-RAY DIFFRACTIONr_long_range_B_other5.18223.3087697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 267 -
Rwork0.242 5209 -
obs--96.73 %

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