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- PDB-2g9u: The crystal structure of glycogen phosphorylase in complex with (... -

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Basic information

Entry
Database: PDB / ID: 2g9u
TitleThe crystal structure of glycogen phosphorylase in complex with (3R,4R,5R)-5-hydroxymethyl-1-(3-phenylpropyl)-piperidine-3,4-diol and phosphate
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogen phosphorylase / catalytic site / rational inhibitor design
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-G27 / PHOSPHATE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsOikonomakos, N.G. / Tiraidis, C. / Leonidas, D.D. / Zographos, S.E.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Iminosugars as potential inhibitors of glycogenolysis: structural insights into the molecular basis of glycogen phosphorylase inhibition.
Authors: Oikonomakos, N.G. / Tiraidis, C. / Leonidas, D.D. / Zographos, S.E. / Kristiansen, M. / Jessen, C.U. / Norskov-Lauritsen, L. / Agius, L.
History
DepositionMar 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)97,9754
Polymers97,5191
Non-polymers4553
Water3,153175
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9498
Polymers195,0392
Non-polymers9116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6780 Å2
ΔGint-41 kcal/mol
Surface area56510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.522, 128.522, 116.437
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: 97519.320 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-G27 / (3R,4R,5R)-5-(HYDROXYMETHYL)-1-(3-PHENYLPROPYL)PIPERIDINE-3,4-DIOL


Mass: 265.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 287 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH 6.7, SMALL TUBES, temperature 287K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2005
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2.15→90.91 Å / Num. all: 52635 / Num. obs: 52635 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.065 / Net I/σ(I): 14
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 3829 / Rsym value: 0.48 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1HLF

1hlf


Resolution: 2.15→90.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.008 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21844 2665 5.1 %RANDOM
Rwork0.18994 ---
all0.1914 49970 --
obs0.1914 49970 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.177 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.15→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 29 175 6744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226713
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9589086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54423.49341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.241151167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3761559
X-RAY DIFFRACTIONr_chiral_restr0.0770.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025126
X-RAY DIFFRACTIONr_nbd_refined0.1860.22896
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2308
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.23
X-RAY DIFFRACTIONr_mcbond_it0.5881.54122
X-RAY DIFFRACTIONr_mcangle_it1.02226451
X-RAY DIFFRACTIONr_scbond_it1.28332955
X-RAY DIFFRACTIONr_scangle_it2.1284.52635
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 204 -
Rwork0.253 3625 -
obs-3829 98.26 %

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