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- PDB-3amv: ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ... -

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Basic information

Entry
Database: PDB / ID: 3amv
TitleALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ANTIDIABETIC DRUG
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE)
KeywordsTRANSFERASE / DIABETES / GLYCOGEN METABOLISM / PHOSPHORYLASE A / INHIBITION / ALLOSTERIC SITE
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-BIN / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsOikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T.
Citation
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-tricarbo xylate.
Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H.
#1: Journal: To be Published
Title: Effects of Commonly Used Cryoprotectants on Glycogen Phosphorylase Activity and Structure
Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.J.
#2: Journal: Structure / Year: 1997
Title: The Structure of Glycogen Phosphorylase B with an Alkyl-Dihydropyridine- 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. / Goldman, S. / Schramm, M. / Watson, K.A. / Johnson, L.N.
History
DepositionFeb 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 26, 1999Provider: 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2975
Polymers97,3711
Non-polymers9264
Water13,565753
1
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,59510
Polymers194,7422
Non-polymers1,8528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10760 Å2
ΔGint-36 kcal/mol
Surface area55880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.200, 127.200, 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

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein PROTEIN (GLYCOGEN PHOSPHORYLASE)


Mass: 97371.180 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-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-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

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Non-polymers , 4 types, 756 molecules

#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: Chemical ChemComp-BIN / 2,3-DICARBOXY-4-(2-CHLORO-PHENYL)-1-ETHYL-5-ISOPROPOXYCARBONYL-6-METHYL-PYRIDINIUM


Mass: 406.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21ClNO6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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 %
Crystal growpH: 6.7
Details: 1 MM W1807 IN A MEDIUM CONSISTING OF 20-24 MG/ML ENZYME, 10 MM MAGNESIUM ACETATE, 3 MM DTT, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (22 DEG C).
Crystal grow
*PLUS
Temperature: 100 K / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMGlc11
21 mMW180711

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→13 Å / Num. obs: 51612 / % possible obs: 92.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.35
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / % possible all: 87.3
Reflection
*PLUS
Num. measured all: 337366
Reflection shell
*PLUS
% possible obs: 87.3 %

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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: 2.1→13 Å / Cross valid method: R FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -5 %RANDOM
Rwork0.189 ---
obs-51612 92.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 61 753 7425
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_deg1.5
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_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
Num. reflection obs: 48964 / Num. reflection Rfree: 2648
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2

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