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- PDB-5o54: Glycogen Phosphorylase b in complex with 29a -

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Basic information

Entry
Database: PDB / ID: 5o54
TitleGlycogen Phosphorylase b in complex with 29a
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-9LB / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsKyriakis, E. / Solovou, T.G.A. / Stravodimos, G.A. / Kantsadi, A.L. / Chatzileontiadou, D.S. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Nanomolar Inhibitors of Glycogen Phosphorylase Based on beta-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study.
Authors: Bokor, E. / Kyriakis, E. / Solovou, T.G.A. / Koppany, C. / Kantsadi, A.L. / Szabo, K.E. / Szakacs, A. / Stravodimos, G.A. / Docsa, T. / Skamnaki, V.T. / Zographos, S.E. / Gergely, P. / ...Authors: Bokor, E. / Kyriakis, E. / Solovou, T.G.A. / Koppany, C. / Kantsadi, A.L. / Szabo, K.E. / Szakacs, A. / Stravodimos, G.A. / Docsa, T. / Skamnaki, V.T. / Zographos, S.E. / Gergely, P. / Leonidas, D.D. / Somsak, L.
History
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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)98,3244
Polymers97,4221
Non-polymers9023
Water4,288238
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6488
Polymers194,8452
Non-polymers1,8036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6950 Å2
ΔGint-29 kcal/mol
Surface area55760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.862, 127.862, 115.731
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) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-9LB / (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(5-phenyl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4-diol


Mass: 306.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O4
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
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
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5419 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.45→13.91 Å / Num. obs: 33526 / % possible obs: 94.2 % / Redundancy: 10.1 % / Rsym value: 0.13 / Net I/σ(I): 17.5
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3345 / Rsym value: 0.775 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
CrysalisProdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.45→13.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.706 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.222 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18706 1678 5 %RANDOM
Rwork0.14405 ---
obs0.1462 31822 93.46 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 28.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.45→13.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 60 238 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196832
X-RAY DIFFRACTIONr_bond_other_d0.0020.026313
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9619264
X-RAY DIFFRACTIONr_angle_other_deg0.937314594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49323.571350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2331559
X-RAY DIFFRACTIONr_chiral_restr0.0740.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021469
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_it2.0241.5793247
X-RAY DIFFRACTIONr_mcbond_other2.0241.5773246
X-RAY DIFFRACTIONr_mcangle_it3.1622.3614056
X-RAY DIFFRACTIONr_mcangle_other3.1622.3624057
X-RAY DIFFRACTIONr_scbond_it3.1021.9883585
X-RAY DIFFRACTIONr_scbond_other3.1011.9883586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8492.8365204
X-RAY DIFFRACTIONr_long_range_B_refined6.1918.687715
X-RAY DIFFRACTIONr_long_range_B_other6.1918.6797716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 124 -
Rwork0.205 2039 -
obs--83.19 %
Refinement TLS params.Method: refined / Origin x: 28.134 Å / Origin y: 21.196 Å / Origin z: 31.464 Å
111213212223313233
T0.0269 Å2-0.0327 Å20.0055 Å2-0.0489 Å2-0.0251 Å2--0.0414 Å2
L0.5453 °20.032 °2-0.0032 °2-0.4323 °2-0.1337 °2--0.8436 °2
S-0.0351 Å °0.0283 Å °0.0368 Å °-0.0089 Å °0.0029 Å °0.0145 Å °0.0508 Å °-0.0913 Å °0.0322 Å °

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