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- PDB-3zcq: Rabbit muscle glycogen phosphorylase b in complex with N-(4- trif... -

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Basic information

Entry
Database: PDB / ID: 3zcq
TitleRabbit muscle glycogen phosphorylase b in complex with N-(4- trifluoromethyl-benzoyl)-N-beta-D-glucopyranosyl urea determined at 2. 15 A resolution
ComponentsGLYCOGEN PHOSPHORYLASE, MUSCLE FORM
KeywordsTRANSFERASE / INHIBITOR / 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
Chem-62N / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)98,1594
Polymers97,4221
Non-polymers7363
Water5,062281
1
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules

A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3188
Polymers194,8452
Non-polymers1,4736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6290 Å2
ΔGint-34.9 kcal/mol
Surface area57440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.650, 128.650, 116.903
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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-62N / N-{[4-(trifluoromethyl)benzoyl]carbamoyl}-beta-D-glucopyranosylamine


Mass: 394.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17F3N2O7
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: SRS / Beamline: PX9.6 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 53088 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.1 / % possible all: 99.5

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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: 2.15→29.59 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.362 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.177 / 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, 252-257, 315-323, 837-842
RfactorNum. reflection% reflectionSelection details
Rfree0.21743 2699 5.1 %RANDOM
Rwork0.1818 ---
obs0.18365 50377 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.528 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 47 281 6909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226775
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9599175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50523.555346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.398151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6561559
X-RAY DIFFRACTIONr_chiral_restr0.0710.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215190
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_it0.4911.54032
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94926509
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28432743
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2514.52666
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: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 225 -
Rwork0.213 3645 -
obs--99.15 %

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