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- PDB-6r0h: Glycogen Phosphorylase b in complex with 3 -

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Basic information

Entry
Database: PDB / ID: 6r0h
TitleGlycogen Phosphorylase b in complex with 3
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-JN2 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsTsagkarakou, S.A. / Koulas, M.S. / Kyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: Molecules / Year: 2019
Title: High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d- ...Title: High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors.
Authors: Fischer, T. / Koulas, S.M. / Tsagkarakou, A.S. / Kyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Riedl, R. / Leonidas, D.D.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 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)98,0473
Polymers97,4221
Non-polymers6252
Water3,855214
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,0946
Polymers194,8452
Non-polymers1,2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5510 Å2
ΔGint-23 kcal/mol
Surface area56610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.287, 128.287, 116.120
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-1212-

HOH

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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-JN2 / 3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide


Mass: 377.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FNO6
#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.: 214 / 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: 49.84 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / 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 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.5→13.71 Å / Num. obs: 32589 / % possible obs: 96.1 % / Redundancy: 3.7 % / CC1/2: 0.977 / Rsym value: 0.11 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3644 / CC1/2: 0.563 / Rsym value: 0.754 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrysalisProdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→13.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.56 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.258 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21278 1610 4.9 %RANDOM
Rwork0.15903 ---
obs0.16174 30957 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 29.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.5→13.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 42 214 6845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136781
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176287
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.659181
X-RAY DIFFRACTIONr_angle_other_deg1.3021.57814525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33521.576406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.212151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2761559
X-RAY DIFFRACTIONr_chiral_restr0.0750.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021522
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_it1.9611.6013237
X-RAY DIFFRACTIONr_mcbond_other1.9551.63236
X-RAY DIFFRACTIONr_mcangle_it3.1542.3954041
X-RAY DIFFRACTIONr_mcangle_other3.1542.3964042
X-RAY DIFFRACTIONr_scbond_it3.0481.9913544
X-RAY DIFFRACTIONr_scbond_other3.0481.9913545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7862.8435141
X-RAY DIFFRACTIONr_long_range_B_refined6.17718.627474
X-RAY DIFFRACTIONr_long_range_B_other6.17718.6217475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 99 -
Rwork0.256 2105 -
obs--88.69 %
Refinement TLS params.Method: refined / Origin x: 28.206 Å / Origin y: 21.251 Å / Origin z: 31.559 Å
111213212223313233
T0.0978 Å2-0.0324 Å20.0051 Å2-0.1239 Å2-0.0247 Å2--0.0098 Å2
L0.6209 °20.0668 °20.0545 °2-0.463 °2-0.1671 °2--0.8384 °2
S-0.0357 Å °0.0161 Å °0.0512 Å °-0.0055 Å °0.0069 Å °0.004 Å °0.0279 Å °-0.0805 Å °0.0288 Å °

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