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- PDB-1h5u: THE 1.76 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE... -

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Basic information

Entry
Database: PDB / ID: 1h5u
TitleTHE 1.76 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE B COMPLEXED WITH GLUCOSE AND CP320626, A POTENTIAL ANTIDIABETIC DRUG
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsGLYCOGEN METABOLISM / GLYCOGEN PHOSPHORYLASE B / INHIBITION / CENTRAL CAVITY / DRUG BINDING SITE / TRANSFERASE
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-CHI / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsOikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Archontis, G.
Citation
Journal: Bioorg.Med.Chem. / Year: 2002
Title: The 1.76 A Resolution Crystal Structure of Glycogen Phosphorylase B Complexed with Glucose, and Cp320626, a Potential Antidiabetic Drug
Authors: Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Archontis, G.
#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.
History
DepositionMay 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 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 1.6Dec 13, 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)98,1624
Polymers97,2911
Non-polymers8713
Water6,395355
1
A: GLYCOGEN PHOSPHORYLASE
hetero molecules

A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3258
Polymers194,5822
Non-polymers1,7426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)128.966, 128.966, 116.186
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 / / 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
#2: Chemical ChemComp-CHI / 5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID [1-(4-FLUOROBENZYL)-2-(4-HYDROXYPIPERIDIN-1YL)-2-OXOETHYL]AMIDE


Mass: 443.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClFN3O3
#3: 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
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986. HIGH RESOLUTION ...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: 2.48 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.7
Details: PHOSPHORYLASE B-GLC-CP320626 COMPLEX WAS CO-CRYSTALLISED UNDER CONDITIONS SIMILAR TO THOSE DESCRIBED BY OIKONOMAKOS ET AL., (2000) STRUCTURE 8, 575-584., pH 6.70
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6.7 / Method: unknown
Details: Zographos, S.E., (1997) Structure (London), 5, 1413.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMW180711
227-28 mg/mlenzyme11
31 mMspermine11
43 mMdithiothreitol11
510 mMBES11
60.1 mMEDTA11
70.02 %sodium azide11

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.05
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.76→26.25 Å / Num. obs: 93061 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.41
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.33 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 483106
Reflection shell
*PLUS
% possible obs: 94.8 % / Mean I/σ(I) obs: 2.33

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C50

1c50


Resolution: 1.76→26.25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: RESIDUES WHERE B-FACTOR VALUES OF MAIN CHAIN ATOMS EXCEED 60 A2 INCLUDE 13-17, 209-211, 250-254, 260, 313-314, 324-325, 550-557, AND 831-837. THE SAME RESIDUES ARE ALSO POORLY ORDERED IN THE ...Details: RESIDUES WHERE B-FACTOR VALUES OF MAIN CHAIN ATOMS EXCEED 60 A2 INCLUDE 13-17, 209-211, 250-254, 260, 313-314, 324-325, 550-557, AND 831-837. THE SAME RESIDUES ARE ALSO POORLY ORDERED IN THE NATIVE ENZYME STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4663 5 %RANDOM
Rwork0.211 ---
obs0.211 92971 95.8 %-
Refinement stepCycle: LAST / Resolution: 1.76→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6591 0 58 355 7004
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68
LS refinement shell
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 1.79 Å / Rfactor Rfree: 0.366 / Rfactor Rwork: 0.342

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