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- PDB-1hlf: BINDING OF GLUCOPYRANOSYLIDENE-SPIRO-THIOHYDANTOIN TO GLYCOGEN PH... -

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Basic information

Entry
Database: PDB / ID: 1hlf
TitleBINDING OF GLUCOPYRANOSYLIDENE-SPIRO-THIOHYDANTOIN TO GLYCOGEN PHOSPHORYLASE B: KINETIC AND CRYSTALLOGRAPHIC STUD
ComponentsGLYCOGEN 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
Chem-GL4 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.26 Å
AuthorsOikonomakos, N.G. / Skamnaki, V.T. / Docsa, T. / Toth, B. / Gergely, P. / Osz, E. / Szilagyi, L. / Somsak, L.
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: Tetrahedron Lett. / Year: 1995
Title: Potent Inhibition of Glycogen Phosphorylase by a Spirohydantoin of Glucopyranose: First Pyranose Analogues of Hydantocidin
Authors: Bichard, C.J. / Mitchell, E.P. / Wormald, M.R. / Watson, K.A. / Johnson, L.N. / Zographos, S.E. / Koutra, D.D. / Oikonomakos, N.G. / Fleet, G.W.
#2: 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.
History
DepositionDec 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8033
Polymers97,2911
Non-polymers5112
Water4,378243
1
A: GLYCOGEN PHOSPHORYLASE
hetero molecules

A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6056
Polymers194,5822
Non-polymers1,0234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7380 Å2
ΔGint-28 kcal/mol
Surface area58770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.787, 128.787, 116.169
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) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Sugar ChemComp-GL4 / (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-thioxo-6-oxa-1,3-diazaspiro[4.5]decan-4-one / 8,9,10-TRIHYDROXY-7-HYDROXYMETHYL-2-THIOXO-6-OXA-1,3-DIAZA-SPIRO[4.5]DECAN-4-ONE


Type: D-saccharide / Mass: 264.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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 growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: CRYSTALLIZATION CONDITIONS: 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 70 MM ...Details: CRYSTALLIZATION CONDITIONS: 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 70 MM CONCENTRATION OF THE COMPOUND, pH 6.70, SMALL TUBES, temperature 289K
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 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 1996
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→28.06 Å / Num. obs: 45104 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 2.26→2.3 Å / Rmerge(I) obs: 0.158 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 255617
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 5.5

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Processing

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

2prj


Resolution: 2.26→28.06 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2278 5 %RANDOM
Rwork0.193 ---
obs0.193 45104 97.4 %-
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.26→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 32 243 7024
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_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
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
LS refinement shellResolution: 2.26→28.06 Å
RfactorNum. reflection% reflection
Rfree0.221 2278 -
Rwork0.193 --
obs-45104 97 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75
LS refinement shell
*PLUS
Rfactor Rfree: 0.221 / Rfactor Rwork: 0.193

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