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- PDB-1ggn: Structures of glycogen phosphorylase-inhibitor complexes and the ... -

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Basic information

Entry
Database: PDB / ID: 1ggn
TitleStructures of glycogen phosphorylase-inhibitor complexes and the implications for structure-based drug design
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE)
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / INHIBITOR COMPLEX / CATALYTIC SITE / DESIGN
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
BETA-D-GLUCOPYRANOSE SPIROHYDANTOIN / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.36 Å
AuthorsWatson, K.A. / Tsitsanou, K.E. / Gregoriou, M. / Zographos, S.E. / Skamnaki, V.T. / Oikonomakos, N.G. / Fleet, G.W. / Johnson, L.N.
Citation
Journal: Bioorg.Med.Chem. / Year: 2002
Title: Kinetic and crystallographic studies of glucopyranosylidene spirothiohydantoin binding to glycogen phosphorylase B.
Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Osz, E. / Szilagyi, L. / Somsak, L. / Docsa, T. / Toth, B. / Gergely, P.
#1: Journal: Protein Sci. / Year: 1998
Title: The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100K: The Role of the Water Structure and its Contribution to Binding
Authors: Gregoriou, M. / Noble, M.E. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / de la Fuente, C. / Fleet, G.W. / Oikonomakos, N.G. / Johnson, L.N.
#2: Journal: Tetrahedron Lett. / Year: 1995
Title: Potent Inhibition of Glycogen Phosphorylase by a Spirohydantoin of Glucopyranose: First Pyranose Analogues of Hydantocidin
Authors: Bichard, C.J.F. / Mitchell, E.P. / Wormald, M.R. / Watson, K.A. / Johnson, L.N. / Zographos, S.E. / Koutra, D.D. / Oikonomakos, N.G. / Fleet, G.W.J.
#3: Journal: Protein Sci. / Year: 1995
Title: N-Acetyl-Beta-D-Glucopyranosylamine: A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose
Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R.
#4: Journal: Biochemistry / Year: 1994
Title: Design of Inhibitors of Glycogen Phosphorylase: A Study of Alpha- and Beta-C-Glucosides and 1-Thio-Beta-D-Glucose Compounds
Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J. / Orchard, M.G. / Fleet, G.W. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgiou, A.C.
History
DepositionAug 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Category: struct_conn / struct_site / struct_site_gen / Item: _struct_conn.pdbx_leaving_atom_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7873
Polymers97,2911
Non-polymers4952
Water3,963220
1
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5736
Polymers194,5822
Non-polymers9914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7260 Å2
ΔGint-21 kcal/mol
Surface area58850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.500, 128.500, 116.300
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 PROTEIN (GLYCOGEN PHOSPHORYLASE)


Mass: 97291.203 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: Sugar ChemComp-GLS / BETA-D-GLUCOPYRANOSE SPIROHYDANTOIN


Type: D-saccharide / Mass: 248.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H12N2O7
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 48 %
Crystal growpH: 6.7
Details: T-STATE GPB CRYSTALS (OIKONOMAKOS ET AL., 1985, BBA 832, 248) WERE SOAKED FOR 1 H IN A BUFFERED SOLUTION [10 MM BES, 0.1 MM EDTA, PH 6.7] CONTAINING A 100 MM CONCENTRATION OF THE COMPOUND. , pH 6.70
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Details: Oikonomakos, N.G., (1985) Biochim.Biophys.Acta., 832, 248.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127.5 mg/mlphosphorylase b11
210 mMBes11
32.9 mMdithiothreitol11
40.1 mMEDTA11
51.1 mMspermine11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: NICOLET / Detector: AREA DETECTOR / Date: Nov 11, 1994
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→14.8 Å / Num. obs: 31588 / % possible obs: 78.2 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.36→2.47 Å
Reflection
*PLUS
Highest resolution: 2.36 Å / Lowest resolution: 14.8 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
CCP4model building
X-PLOR3.851refinement
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: 2PRJ

2prj


Resolution: 2.36→14.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1595 5 %RANDOM
Rwork0.189 ---
obs0.189 31588 78.2 %-
Refinement stepCycle: LAST / Resolution: 2.36→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 32 220 7001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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