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- PDB-6qa6: Glycogen Phosphorylase b in complex with 30 -

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Basic information

Entry
Database: PDB / ID: 6qa6
TitleGlycogen Phosphorylase b in complex with 30
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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-HT8 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsKyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography.
Authors: Szabo, K.E. / Kyriakis, E. / Psarra, A.G. / Karra, A.G. / Sipos, A. / Docsa, T. / Stravodimos, G.A. / Katsidou, E. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Mandi, A. / Kiraly, S. ...Authors: Szabo, K.E. / Kyriakis, E. / Psarra, A.G. / Karra, A.G. / Sipos, A. / Docsa, T. / Stravodimos, G.A. / Katsidou, E. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Mandi, A. / Kiraly, S.B. / Kurtan, T. / Leonidas, D.D. / Somsak, L.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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)98,4645
Polymers97,4221
Non-polymers1,0424
Water4,107228
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,92910
Polymers194,8452
Non-polymers2,0848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6650 Å2
ΔGint-18 kcal/mol
Surface area56400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.161, 128.161, 115.794
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: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-HT8 / (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one


Mass: 358.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N2O6
#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.: 228 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5419 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.4→13.69 Å / Num. obs: 33997 / % possible obs: 90.3 % / Redundancy: 5.8 % / CC1/2: 0.997 / Rsym value: 0.074 / Net I/σ(I): 16.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2975 / CC1/2: 0.925 / Rsym value: 0.402 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→13.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.259 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.234 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19894 1658 4.9 %RANDOM
Rwork0.14082 ---
obs0.14366 32266 88.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 27.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-0 Å2
2--0.25 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.4→13.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 71 228 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0146822
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176075
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6619244
X-RAY DIFFRACTIONr_angle_other_deg0.9611.63414227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08321.52408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3021560
X-RAY DIFFRACTIONr_chiral_restr0.0770.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021294
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_it2.0811.6313239
X-RAY DIFFRACTIONr_mcbond_other2.081.6293238
X-RAY DIFFRACTIONr_mcangle_it3.22.4384044
X-RAY DIFFRACTIONr_mcangle_other3.22.4394045
X-RAY DIFFRACTIONr_scbond_it3.3722.0653583
X-RAY DIFFRACTIONr_scbond_other3.3722.0663584
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0692.9435200
X-RAY DIFFRACTIONr_long_range_B_refined6.25919.17676
X-RAY DIFFRACTIONr_long_range_B_other6.25619.0237646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 106 -
Rwork0.213 1972 -
obs--74.56 %
Refinement TLS params.Method: refined / Origin x: 28.192 Å / Origin y: 21.252 Å / Origin z: 31.478 Å
111213212223313233
T0.0246 Å2-0.0315 Å20.0058 Å2-0.0504 Å2-0.0208 Å2--0.0272 Å2
L0.586 °20.0483 °20.004 °2-0.4371 °2-0.1172 °2--0.8981 °2
S-0.0174 Å °0.0382 Å °0.0378 Å °-0.0055 Å °-0.0071 Å °0.0118 Å °0.0519 Å °-0.0813 Å °0.0245 Å °

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