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- PDB-2qn8: Glycogen Phosphorylase b in complex with N-4-nitrobenzoyl-N'-beta... -

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Basic information

Entry
Database: PDB / ID: 2qn8
TitleGlycogen Phosphorylase b in complex with N-4-nitrobenzoyl-N'-beta-D-glucopyranosyl urea
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate
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-NBY / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsChrysina, E.D. / Tiraidis, C. / Alexacou, K.-M. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G.
CitationJournal: To be Published
Title: N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation
Authors: Nagy, V. / Felf ldi, N. / Praly, J.-P. / Dosca, T. / Gergerly, P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M.N. / Alexacou, K.-M. / Konstantakaki, M.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 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, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3775
Polymers97,2911
Non-polymers1,0864
Water5,945330
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,75410
Polymers194,5822
Non-polymers2,1728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.612, 128.612, 116.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1222-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: Sugar ChemComp-NBY / N-{[(4-nitrophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine / N-{[(4-nitrophenyl)carbonyl]carbamoyl}-beta-D-glucosylamine / N-{[(4-nitrophenyl)carbonyl]carbamoyl}-D-glucosylamine / N-{[(4-nitrophenyl)carbonyl]carbamoyl}-glucosylamine


Type: D-saccharide / Mass: 371.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17N3O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT RESIDUE 380 WAS AN ILE ACCORDING TO THE ELECTRON DENSITY.

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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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes, 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: X11 / Wavelength: 0.8468 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 65665 / Num. obs: 65665 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.055 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3649 / Rsym value: 0.501 / % possible all: 96.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2PRJ

2prj


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3735 -RANDOM
Rwork0.181 ---
obs-65665 94.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6569 0 72 330 6971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbonds0.005
X-RAY DIFFRACTIONangles1.23
LS refinement shellResolution: 1.9→1.94 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.286

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