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- PDB-2g9v: The crystal structure of glycogen phosphorylase in complex with (... -

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Basic information

Entry
Database: PDB / ID: 2g9v
TitleThe crystal structure of glycogen phosphorylase in complex with (3R,4R,5R)-5-hydroxymethylpiperidine-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 / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / 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 1.3Jul 8, 2015Group: Non-polymer description
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.5Nov 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)97,8564
Polymers97,5191
Non-polymers3373
Water4,035224
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7138
Polymers195,0392
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6130 Å2
ΔGint-38 kcal/mol
Surface area57150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.636, 128.636, 116.455
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: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
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: 51324 / Num. obs: 51324 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.076 / Net I/σ(I): 9.5
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3850 / Rsym value: 0.481 / % 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: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.331 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23501 2587 5 %RANDOM
Rwork0.19347 ---
all0.19557 48722 --
obs0.19557 48722 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.093 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.195 Å0.138 Å
Refinement stepCycle: LAST / Resolution: 2.15→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6579 0 20 224 6823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226744
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9569128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1715803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24823.488344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.098151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2191559
X-RAY DIFFRACTIONr_chiral_restr0.0770.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025153
X-RAY DIFFRACTIONr_nbd_refined0.1890.22970
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2342
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.24
X-RAY DIFFRACTIONr_mcbond_it0.5971.54144
X-RAY DIFFRACTIONr_mcangle_it1.03526484
X-RAY DIFFRACTIONr_scbond_it1.26432967
X-RAY DIFFRACTIONr_scangle_it2.0844.52644
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 169 -
Rwork0.25 3681 -
obs-3850 98.59 %

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