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- PDB-3zcu: Rabbit muscle glycogen phosphorylase b in complex with N-(pyridyl... -

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Basic information

Entry
Database: PDB / ID: 3zcu
TitleRabbit muscle glycogen phosphorylase b in complex with N-(pyridyl-2- carbonyl)-N-beta-D-glucopyranosyl urea determined at 2.05 A resolution
ComponentsGLYCOGEN PHOSPHORYLASE, MUSCLE FORM
KeywordsTRANSFERASE / N-ACYL-N-BETA-D-GLUCOPYRANOSYL UREAS / INHIBITORS / HYPOGLYCAEMIC AGENTS / STRUCTURE BASED LIGAND DESIGN
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
PYRIDOXAL-5'-PHOSPHATE / Chem-T68 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. ...Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. / Konstantakaki, M. / Kardakaris, R. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. / Somsak, L.
Citation
Journal: To be Published
Title: Synthesis, Kinetic, Computational and Crystallographic Evaluation of N-Acyl-N-Beta-D- Glucopyranosyl)Ureas, Nanomolar Glucose Analogue Inhibitors of Glycogen Phosphorylase, Potential Antidiabetic Agents
Authors: Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. / Konstantakaki, M. / Kardakaris, R. / Leonidas, D.D. ...Authors: Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. / Konstantakaki, M. / Kardakaris, R. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. / Somsak, L.
#1: Journal: Eur.J.Biochem. / Year: 2002
Title: Binding of N-Acetyl-N '-Beta-D-Glucopyranosyl Urea and N-Benzoyl-N '-Beta-D-Glucopyranosyl Urea to Glycogen Phosphorylase B: Kinetic and Crystallographic Studies.
Authors: Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J. / Docsa, T. / Toth, B. / Gergely, P.
History
DepositionNov 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _pdbx_database_status.status_code_sf / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9973
Polymers97,4221
Non-polymers5742
Water5,080282
1
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules

A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9946
Polymers194,8452
Non-polymers1,1494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5470 Å2
ΔGint-20.8 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.414, 128.414, 116.523
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: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RABBIT SKELETAL MUSCLE / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-T68 / N-[(pyridin-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine / N-[(pyridin-2-ylcarbonyl)carbamoyl]-beta-D-glucosylamine / N-[(pyridin-2-ylcarbonyl)carbamoyl]-D-glucosylamine / N-[(pyridin-2-ylcarbonyl)carbamoyl]-glucosylamine


Type: D-saccharide / Mass: 327.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N3O7
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 6.8 / Details: pH 6.8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Feb 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 61537 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QNB

2qnb


Resolution: 2.05→24.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.828 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES WERE NOT INCLUDED IN THE STRUCTURE SINCE THERE WAS NOT SUFFICIENT DENSITY TO INDICATE THEIR POSITION 1-11, 252-260, 315-323, 837-842
RfactorNum. reflection% reflectionSelection details
Rfree0.21588 3113 5.1 %RANDOM
Rwork0.18514 ---
obs0.1867 58355 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6569 0 38 282 6889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9589147
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66523.536345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.232151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7171559
X-RAY DIFFRACTIONr_chiral_restr0.0720.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215181
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4871.54024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94926498
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28432732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2544.52649
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 236 -
Rwork0.234 4207 -
obs--99.96 %

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