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- PDB-1gfz: FLAVOPIRIDOL INHIBITS GLYCOGEN PHOSPHORYLASE BY BINDING AT THE IN... -

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Basic information

Entry
Database: PDB / ID: 1gfz
TitleFLAVOPIRIDOL INHIBITS GLYCOGEN PHOSPHORYLASE BY BINDING AT THE INHIBITOR SITE
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / DIABETES / FLAVOPIRIDOL / INHIBITOR SITE
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
CAFFEINE / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 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: Structure / Year: 2000
Title: A New Allosteric Site in Glycogen Phosphorylase b as a Target for Drug Interactions
Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Tsitsanou, K.E. / Gavalas, N.G. / Johnson, L.N.
#2: 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.
History
DepositionJun 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 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_ref_seq_dif / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0814
Polymers97,2911
Non-polymers7903
Water3,657203
1
A: GLYCOGEN PHOSPHORYLASE
hetero molecules

A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1618
Polymers194,5822
Non-polymers1,5796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7610 Å2
ΔGint-30 kcal/mol
Surface area56880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.296, 128.296, 116.377
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 /


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: 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-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE / Caffeine (data page)


Mass: 194.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.7
Details: A single native T-state GPb crystal was soaked in a solution containing 5 mM caffeine, 10 mM Bes, 0.1 mM EDTA buffer, pH 6.7 for 80 min, pH 6.70, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: unknown
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 mMspermine(GPa)11or 10 mM magnesium acetate
850 mMglucose11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 27, 2000
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.75 Å / Num. obs: 43063 / % possible obs: 98.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.8 / % possible all: 94
Reflection
*PLUS
Num. measured all: 310740 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→28.75 Å / Cross valid method: R FREE / σ(F): 0
Details: the final model contains residues 13-256, 261-316, and 324-837. Residues where B-factor values of main chain atoms exceed 60^2 include 13-22, 209-211, 250-256, 313-316, 324-325, 550-557, and ...Details: the final model contains residues 13-256, 261-316, and 324-837. Residues where B-factor values of main chain atoms exceed 60^2 include 13-22, 209-211, 250-256, 313-316, 324-325, 550-557, and 831-837. Thes same regions are also poorly ordered in the native enzyme structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 -5 %RANDOM
Rwork0.189 ---
obs0.189 43030 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 52 203 6879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.31
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_improper_angle_d0.71
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / Rfactor Rwork: 0.328

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