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- PDB-2qn2: Glycogen Phosphorylase b in complex with Maslinic Acid -

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Basic information

Entry
Database: PDB / ID: 2qn2
TitleGlycogen Phosphorylase b in complex with Maslinic Acid
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / APOPTOSIS / glycogenolysis / type 2 diabetes
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
maslinic acid / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.698 Å
AuthorsZographos, S.E. / Leonidas, D.D. / Alexacou, K.-M. / Hayes, J. / Oikonomakos, N.G.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Naturally occurring pentacyclic triterpenes as inhibitors of glycogen phosphorylase: synthesis, structure-activity relationships, and X-ray crystallographic studies
Authors: Wen, X. / Sun, H. / Liu, J. / Cheng, K. / Zhang, P. / Zhang, L. / Hao, J. / Zhang, L. / Ni, P. / Zographos, S.E. / Leonidas, D.D. / Alexacou, K.-M. / Gimisis, T. / Hayes, J.M. / Oikonomakos, N.G.
History
DepositionJul 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9902
Polymers97,5191
Non-polymers4711
Water2,324129
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9804
Polymers195,0392
Non-polymers9412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6230 Å2
ΔGint-23 kcal/mol
Surface area57220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.718, 128.718, 116.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimeric glycogen phosphorylase is the physiologically active species. The second part of the biological assembly is generated by the two fold axis: y, x, 1-z 7_556

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Components

#1: Protein Glycogen phosphorylase, muscle form / / E.C.2.4.1.1 / Glycogen Phosphorylase b / Myophosphorylase


Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle, gene PYGM / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-0MA / maslinic acid / (2beta,3beta,5beta,18alpha)-2,3-dihydroxyoleana-12,21-dien-28-oic acid / Maslinic acid


Mass: 470.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H46O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 2.698→90.91 Å / Num. all: 27542 / Num. obs: 27542 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.077 / Net I/σ(I): 17.2
Reflection shellResolution: 2.698→2.75 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.492 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2PRJ

2prj


Resolution: 2.698→90.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.204 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22268 1383 5 %RANDOM
Rwork0.16769 ---
all0.17041 26130 --
obs0.17041 26130 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.303 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--1.18 Å20 Å2
3----2.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.312 Å
Refinement stepCycle: LAST / Resolution: 2.698→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 34 129 6801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226826
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9589253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6235810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.223.486350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.138151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9131560
X-RAY DIFFRACTIONr_chiral_restr0.0870.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025220
X-RAY DIFFRACTIONr_nbd_refined0.1960.22950
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0630.23
X-RAY DIFFRACTIONr_mcbond_it0.5961.54136
X-RAY DIFFRACTIONr_mcangle_it1.08126534
X-RAY DIFFRACTIONr_scbond_it1.30533019
X-RAY DIFFRACTIONr_scangle_it2.2394.52719
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 87 -
Rwork0.237 1903 -
obs--98.91 %

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