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- PDB-1c50: IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF A NOVEL ALLOSTE... -

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Basic information

Entry
Database: PDB / ID: 1c50
TitleIDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF A NOVEL ALLOSTERIC BINDING SITE OF GLYCOGEN PHOSPHORYLASE B
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE)
KeywordsTRANSFERASE / GLYCOGEN METABOLISM / GLYCOGEN PHOSPHORYLASE B / INHIBITION / CENTRAL CAVITY / DRUG BINDING 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
Chem-CHI / 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. / Skamnaki, V.T. / Tsitsanou, K.E. / Gavalas, N.G. / Johnson, L.N.
Citation
Journal: Structure Fold.Des. / 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.
#1: 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.
#2: Journal: Structure / Year: 1997
Title: The Structure of Glycogen Phosphorylase b with an Alkyldihydropyridine-Dicarboxylic Acid Compound, A Novel and Potent Inhibitor
Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldmann, S. / Watson, K.A. / Johnson, L.N.
History
DepositionDec 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5253
Polymers95,8341
Non-polymers6912
Water4,612256
1
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,0496
Polymers191,6672
Non-polymers1,3824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)129.174, 127.174, 116.220
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: 95833.562 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-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-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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.49 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.7
Details: PHOSPHORYLASE B-CP320626 COMPLEX WAS CO-CRYSTALLISED UNDER CONDITIONS SIMILAR TO THOSE DESCRIBED BY ZOGRAPHOS ET AL., (1997) STRUCTURE 5, 1413-1425., pH 6.7
Crystal grow
*PLUS
Temperature: 16 ℃ / 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: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 42617 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.7 / % possible all: 91
Reflection
*PLUS
Num. measured all: 160475 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 91 %

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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→30 Å / Cross valid method: R FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 -5 %RANDOM
Rwork0.199 ---
obs0.199 40437 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 46 256 7051
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_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
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
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / Num. reflection Rfree: 2162 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2

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