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- PDB-5lrf: Crystal structure of Glycogen Phosphorylase b in complex with KS389 -

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Basic information

Entry
Database: PDB / ID: 5lrf
TitleCrystal structure of Glycogen Phosphorylase b in complex with KS389
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein
Function / homology
Function and homology information


maltodextrin phosphorylase activity / 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-KS3 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsKantsadi, A.L. / Leonidas, D.D.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase.
Authors: Kantsadi, A.L. / Stravodimos, G.A. / Kyriakis, E. / Chatzileontiadou, D.S.M. / Solovou, T.G.A. / Kun, S. / Bokor, E. / Somsak, L. / Leonidas, D.D.
History
DepositionAug 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Revision 1.3Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)98,4096
Polymers97,2911
Non-polymers1,1185
Water5,747319
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,81912
Polymers194,5822
Non-polymers2,23610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6760 Å2
ΔGint-12 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.560, 128.560, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1316-

HOH

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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) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-KS3 / (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4,5-triol


Mass: 357.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N3O5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM BES buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.75→38.38 Å / Num. obs: 90698 / % possible obs: 93.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.9 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→37.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.196 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18507 4430 4.9 %RANDOM
Rwork0.1653 ---
obs0.16628 85955 11.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.502 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.42 Å2
Refinement stepCycle: 1 / Resolution: 1.75→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 75 319 6984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196826
X-RAY DIFFRACTIONr_bond_other_d0.0010.026512
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9639246
X-RAY DIFFRACTIONr_angle_other_deg0.895314907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08923.534348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.613151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0291559
X-RAY DIFFRACTIONr_chiral_restr0.0920.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021666
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 330 -
Rwork0.282 6452 -
obs--94.63 %

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