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- PDB-1z62: Indirubin-3'-aminooxy-acetate inhibits glycogen phosphorylase by ... -

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Basic information

Entry
Database: PDB / ID: 1z62
TitleIndirubin-3'-aminooxy-acetate inhibits glycogen phosphorylase by binding at the inhibitor and the allosteric site. Broad specificities of the two sites
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes
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
Chem-IAA / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKosmopoulou, M.N. / Leonidas, D.D. / Chrysina, E.D. / Eisenbrand, G. / Oikonomakos, N.G.
Citation
Journal: LETT.DRUG DES.DISCOVERY / Year: 2005
Title: Indirubin-3'-Aminooxy-Acetate Inhibits Glycogen Phosphorylase by Binding at the Inhibitor and the Allosteric Site. Broad Specificities of the Two Sites
Authors: Kosmopoulou, M.N. / Leonidas, D.D. / Chrysina, E.D. / Eisenbrand, G. / Oikonomakos, N.G.
#1: Journal: Eur.J.Biochem. / Year: 2004
Title: Binding of the potential antitumour agent indirubin-5-sulphonate at the inhibitor site of rabbit muscle glycogen phosphorylase b. Comparison with ligand binding to pCDK2-cyclin A complex
Authors: Kosmopoulou, M.N. / Leonidas, D.D. / Chrysina, E.D. / Bischler, N. / Eisenbrand, G. / Sakarellos, C.E. / Pauptit, R. / Oikonomakos, N.G.
#2: Journal: Structure / Year: 1997
Title: The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor
Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldmann, S. / Watson, K.A. / Johnson, L.N.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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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)98,5445
Polymers97,2911
Non-polymers1,2534
Water6,125340
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A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,08910
Polymers194,5822
Non-polymers2,5068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)128.487, 128.487, 116.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimeric glycogen phosphorylase is the physiologiacally active species

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 97291.203 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-IAA / ({[(3E)-2'-OXO-2',7'-DIHYDRO-2,3'-BIINDOL-3(7H)-YLIDENE]AMINO}OXY)ACETIC ACID / 2-{O-[2'-(2-OXO-(2H3H)INDOLE-3-YLIDENE)-(2'H3'H)INDOLE-3'-YLIDENE]-AMINOOXY}-ACETATE


Mass: 335.314 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H13N3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.43 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 291 K / Method: small tubes / pH: 6.7
Details: 10mM Bes buffer, 3mM DDT , pH 6.7, SMALL TUBES, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.95 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 76668 / Num. obs: 76668 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 4.06 / Num. unique all: 11984 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→29.49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3342798.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3889 5.1 %RANDOM
Rwork0.191 ---
obs0.191 76617 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.758 Å2 / ksol: 0.312022 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å20 Å20 Å2
2--3.83 Å20 Å2
3----7.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6573 0 90 340 7003
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 630 5 %
Rwork0.256 11984 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.PARAMPLP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4IAA.PARAMIAA.TOP

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