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- PDB-1e1y: Flavopiridol inhibits glycogen phosphorylase by binding at the in... -

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Basic information

Entry
Database: PDB / ID: 1e1y
TitleFlavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site
ComponentsGLYCOGEN PHOSPHORYLASE, MUSCLE FORM
KeywordsTRANSFERASE / ALLOSTERIC INHIBITION
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-CPB / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / PHOSPHITE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsOikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Tsitsanou, K.E. / Johnson, L.N.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Flavopiridol Inhibits Glycogen Phosphorylase by Binding at the Inhibitor Site
Authors: Oikonomakos, N.G. / Schnier, J.B. / Zographos, S.E. / Skamnaki, V.T. / Tsitsanou, K.E. / Johnson, L.N.
#1: Journal: Protein Sci. / Year: 1999
Title: Allosteric Inhibition of Glycogen Phosphorylase a by the Potential Antidiabetic Drug 3-Isopropyl 4-(2-Chlorophenyl)-1,4-Dihydro-1-Ethyl-2-Methyl-Pyridine-3,5,6-Tricarboxylate
Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H.
#2: Journal: Structure / Year: 1997
Title: The Structure of Glycogen Phosphorylase B with an Alkyl-Dihydropyridine-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. / Goldman, S. / Schramm, M. / Watson, K.A. / Johnson, L.N.
History
DepositionMay 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1995
Polymers97,2911
Non-polymers9084
Water11,602644
1
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules

A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,39910
Polymers194,5822
Non-polymers1,8168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9920 Å2
ΔGint-19.1 kcal/mol
Surface area56260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.759, 126.759, 116.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2024-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 647 molecules

#2: Chemical ChemComp-CPB / 2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE / FLAVOPIRIDOL / Alvocidib


Mass: 401.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClNO5 / Comment: inhibitor, alkaloid*YM
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details2AMV SWALL P00489 1 - 13 NOT IN ATOMS LI REFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK, FEBS LETT. ...2AMV SWALL P00489 1 - 13 NOT IN ATOMS LI REFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986. HIGH RESOLUTION DATA (1.5 ANGSTROMS) REFINEMENT ON T-STATE GLYCOGEN PHOSPHORYLASE (UNPUBLISHED RESULTS) HAS CONFIRMED THAT RESIDUE 609 IS INDEED ALA (NOT PRO).

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.7
Details: AS DESCRIBED PREVIOUSLY BY OIKONOMAKOS ET AL. (1999) PROTEIN SCIENCE 8, 1930-1945., pH 6.70
Crystal grow
*PLUS
Method: co-crystallization
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlenzyme11
21 mMflavopiridol11
33 mMdithiothreitol11
410 mMBes11
50.1 mMEDTA11
60.02 %sodium azide11
71 mMspermine11or 10 mM magnesium acetate
850 mMglucose11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.05
DetectorDate: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.23→29.9 Å / Num. obs: 40691 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.1
Reflection shellResolution: 2.23→2.27 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.4 / % possible all: 84.6
Reflection
*PLUS
Num. measured all: 321450
Reflection shell
*PLUS
% possible obs: 84.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GPA

2gpa


Resolution: 2.23→29.9 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: RESIDUES WHERE OVERALL -FACTOR VALUES EXCEED 60 A**2 INCLUDE 16-22 (71.1), 550-556 (69.4), AND 837-838 (75.9). TER PRO: RESIDUES 1-5,251-259,315-324,839- 842 WERE NOT DEFINED BY ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.252 -5 %RANDOM
Rwork0.195 ---
obs0.195 40691 87.3 %-
Refinement stepCycle: LAST / Resolution: 2.23→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 59 644 7320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65
LS refinement shell
*PLUS
Rfactor Rfree: 0.314 / Rfactor Rwork: 0.252

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