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- PDB-6qa8: Glycogen Phosphorylase b in complex with 28 -

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Basic information

Entry
Database: PDB / ID: 6qa8
TitleGlycogen Phosphorylase b in complex with 28
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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-HTE / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.35 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)97,9783
Polymers97,4221
Non-polymers5552
Water3,981221
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9566
Polymers194,8452
Non-polymers1,1114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5380 Å2
ΔGint-19 kcal/mol
Surface area57120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.233, 128.233, 116.089
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-HTE / (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9,10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one


Mass: 308.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O6
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
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: 2.35→13.44 Å / Num. obs: 37248 / % possible obs: 91.6 % / Redundancy: 4.6 % / CC1/2: 0.993 / Rsym value: 0.073 / Net I/σ(I): 12.4
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3258 / CC1/2: 0.804 / Rsym value: 0.61 / % possible all: 77.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
CrysalisProdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→13.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.698 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.229 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21155 1826 4.9 %RANDOM
Rwork0.15725 ---
obs0.15989 35351 90.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 32.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å2-0 Å2
2--0.2 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.35→13.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 37 221 6813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0146741
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176015
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.669128
X-RAY DIFFRACTIONr_angle_other_deg0.8491.63314088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83321.559404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.528151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2111559
X-RAY DIFFRACTIONr_chiral_restr0.0560.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
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_it2.6211.8883221
X-RAY DIFFRACTIONr_mcbond_other2.6211.8873220
X-RAY DIFFRACTIONr_mcangle_it3.7332.834021
X-RAY DIFFRACTIONr_mcangle_other3.7332.8314022
X-RAY DIFFRACTIONr_scbond_it4.5372.43520
X-RAY DIFFRACTIONr_scbond_other4.5372.3993521
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6983.4025108
X-RAY DIFFRACTIONr_long_range_B_refined7.522.3777590
X-RAY DIFFRACTIONr_long_range_B_other7.49822.3167566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 97 -
Rwork0.253 2168 -
obs--76.24 %
Refinement TLS params.Method: refined / Origin x: 28.115 Å / Origin y: 21.22 Å / Origin z: 31.358 Å
111213212223313233
T0.0402 Å2-0.0398 Å20.0023 Å2-0.0785 Å2-0.0245 Å2--0.0158 Å2
L0.6431 °20.0196 °20.0194 °2-0.5038 °2-0.1716 °2--0.9608 °2
S-0.0456 Å °0.0244 Å °0.0379 Å °-0.0017 Å °0.0159 Å °0.0201 Å °0.0629 Å °-0.1165 Å °0.0297 Å °

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