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- PDB-2off: The crystal structure of Glycogen Phosphorylase b in complex with... -

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Basic information

Entry
Database: PDB / ID: 2off
TitleThe crystal structure of Glycogen Phosphorylase b in complex with a potent allosteric inhibitor
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / Glycogenolysis / type 2 diabetes
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-OFF / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsTiraidis, C. / Alexacou, K.-M. / Zographos, S.E. / Leonidas, D.D. / Gimisis, T. / Oikonomakos, N.G.
CitationJournal: Protein Sci. / Year: 2007
Title: FR258900, a potential anti-hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase
Authors: Tiraidis, C. / Alexacou, K.-M. / Zographos, S.E. / Leonidas, D.D. / Gimisis, T. / Oikonomakos, N.G.
History
DepositionJan 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)97,9762
Polymers97,5191
Non-polymers4561
Water5,224290
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9514
Polymers195,0392
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6360 Å2
ΔGint-24 kcal/mol
Surface area56570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.780, 128.780, 116.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsCoordinates for a complete multimer representing the known biologically significant oligomerization state of the molecule can be generated by applying the transformations below: x,y,z and y,x,1-z

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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-OFF / 2-DEOXY-3,4-BIS-O-[3-(4-HYDROXYPHENYL)PROPANOYL]-L-THREO-PENTARIC ACID / 2,3-BIS((E)-3-(4-HYDROXYPHENYL)ACRYLOYLOXY)PENTANEDIOIC ACID


Mass: 456.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 50.12 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: Bes 10mM, EDTA, DTT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→90.9 Å / Num. all: 48704 / Num. obs: 48704 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32.592 Å2 / Rsym value: 0.107 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.431 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→90.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.859 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21316 2474 5.1 %RANDOM
Rwork0.18372 ---
obs0.18525 46201 97.14 %-
all-46201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.187 Å0.255 Å
Refinement stepCycle: LAST / Resolution: 2.2→90.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 33 290 6927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226798
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9589202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94323.553349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.231559
X-RAY DIFFRACTIONr_chiral_restr0.0770.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025227
X-RAY DIFFRACTIONr_nbd_refined0.1820.22816
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24618
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2343
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.26
X-RAY DIFFRACTIONr_mcbond_it0.5371.54177
X-RAY DIFFRACTIONr_mcangle_it0.91826518
X-RAY DIFFRACTIONr_scbond_it1.22433015
X-RAY DIFFRACTIONr_scangle_it2.0284.52684
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 195 -
Rwork0.203 3242 -
obs--94.61 %

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