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- PDB-1a8i: SPIROHYDANTOIN INHIBITOR OF GLYCOGEN PHOSPHORYLASE -

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Basic information

Entry
Database: PDB / ID: 1a8i
TitleSPIROHYDANTOIN INHIBITOR OF GLYCOGEN PHOSPHORYLASE
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsGLYCOGEN PHOSPHORYLASE / GLUCOPYRANOSE SPIROHYDANTOIN / WATER STRUCTURE / INHIBITOR BINDING / ANTI-HYPERGLYCEMIC AGENT
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
BETA-D-GLUCOPYRANOSE SPIROHYDANTOIN / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.78 Å
AuthorsGregoriou, M. / Noble, M.E.M. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / De La Fuente, C. / Fleet, G.W.J. / Oikonomakos, N.G. / Johnson, L.N.
Citation
Journal: Protein Sci. / Year: 1998
Title: The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: 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.
#1: Journal: Synlett / Year: 1997
Title: Stereospecific Synthesis of Spirohydantoins of Beta-Glucopyranose: Inhibitors of Glycogen Phosphorylase
Authors: Krulle, T.M. / De La Fuente, C. / Watson, K.A. / Gregoriou, M. / Johnson, L.N. / Tsitsanou, K.E. / Zographos, S.E. / Oikonomakos, N.G. / Fleet, G.W.J.
#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: 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.
#4: Journal: Biochemistry / Year: 1991
Title: Glucose Analogue Inhibitors of Glycogen Phosphorylase: The Design of Potential Drugs for Diabetes
Authors: Martin, J.L. / Veluraja, K. / Ross, K. / Johnson, L.N. / Fleet, G.W. / Ramsden, N.G. / Bruce, I. / Orchard, M.G. / Oikonomakos, N.G. / Papageorgiou, A.C. / Leonidas, D.D. / Tsitoura, H.S.
#5: Journal: Glycogen Phosphorylase B: Description of the Protein Structure
Year: 1991
Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N.
History
DepositionMar 25, 1998Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn ...pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag ..._pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: 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

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7682
Polymers97,5191
Non-polymers2481
Water14,322795
1
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules

A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5354
Polymers195,0392
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)127.470, 127.470, 115.800
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 B


Mass: 97519.320 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: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 289 K / pH: 6.7
Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M SODIUM EDTA, 0.02 % SODIUM AZIDE AT 16 DEGREES C. THE CRYSTALS WERE SOAKED IN 0.1 M ...Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M SODIUM EDTA, 0.02 % SODIUM AZIDE AT 16 DEGREES C. THE CRYSTALS WERE SOAKED IN 0.1 M SPIROHYDANTOIN AND CRYOPROTECTED WITH 25% (V/V) MPD (2-METHYL-2,4- PENTANEDIOL)., temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127-28 mg/mlprotein11
21 mMspermine11
310 mMBES11
43 mMdithiothreitol11
50.1 mMEDTA11
60.02 %sodium azide11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 18, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.78→19.9 Å / Num. obs: 78974 / % possible obs: 86.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 16.4
Reflection shellResolution: 1.78→1.87 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 4 / % possible all: 65.7
Reflection
*PLUS
Num. measured all: 198525
Reflection shell
*PLUS
% possible obs: 65.7 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: A 1.5 ANGSTROMS MODEL (E.P.MITCHELL, UNPUBLISHED) AND PDB ENTRY 1GPB

1gpb


Resolution: 1.78→19.9 Å / Cross valid method: FREE R-FACTOR
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3967 5 %RANDOM
Rwork0.182 ---
obs-75007 86.4 %-
Refine analyzeLuzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.78→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 32 797 7512
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 78974 / Rfactor all: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg1.3

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