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- PDB-2qlm: Glycogen phosphorylase in complex with FN67 -

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Basic information

Entry
Database: PDB / ID: 2qlm
TitleGlycogen phosphorylase in complex with FN67
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-F68 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsOikonomakos, N.G. / Chryina, E.D. / Tiraidis, C. / Kosmopoulou, M.N. / Zographos, S.E. / Leonidas, D.D.
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. / Docsa, T. / Gergerly, P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M.N. / Alexacou, K.-M. / Konstantakaki, M.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 25, 2017Group: Atomic model
Revision 1.3Aug 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 1.4Nov 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)97,8602
Polymers97,5191
Non-polymers3401
Water5,152286
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7194
Polymers195,0392
Non-polymers6812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.633, 128.633, 116.545
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, muscle form / Myophosphorylase


Mass: 97519.320 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-F68 / N-{[(4-methylphenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine


Mass: 340.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
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: X31 / Wavelength: 0.8123 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 53619 / Num. obs: 53619 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.085 / Net I/σ(I): 21.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 2561 / Rsym value: 0.444 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.211 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21445 2729 5.1 %RANDOM
Rwork0.18382 ---
all0.18536 50872 --
obs0.18536 50872 93.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.173 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 24 286 6913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226785
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9589185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1615807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23623.524349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.191151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5441560
X-RAY DIFFRACTIONr_chiral_restr0.0740.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025202
X-RAY DIFFRACTIONr_nbd_refined0.1790.22861
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2360
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.25
X-RAY DIFFRACTIONr_mcbond_it0.5291.54174
X-RAY DIFFRACTIONr_mcangle_it0.89126513
X-RAY DIFFRACTIONr_scbond_it1.15533000
X-RAY DIFFRACTIONr_scangle_it1.924.52672
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 184 -
Rwork0.231 3599 -
obs-3599 89.99 %

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