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- PDB-2gm9: Structure of rabbit muscle glycogen phosphorylase in complex with... -

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Basic information

Entry
Database: PDB / ID: 2gm9
TitleStructure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE
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
Chem-3TH / Chem-PLR / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOtterbein, L.R. / Pannifer, A.D. / Tucker, J. / Breed, J. / Oikonomakos, N.G. / Minshull, C. / Rowsell, S. / Pauptit, R.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Novel thienopyrrole glycogen phosphorylase inhibitors: synthesis, in vitro SAR and crystallographic studies.
Authors: Whittamore, P.R. / Addie, M.S. / Bennett, S.N. / Birch, A.M. / Butters, M. / Godfrey, L. / Kenny, P.W. / Morley, A.D. / Murray, P.M. / Oikonomakos, N.G. / Otterbein, L.R. / Pannifer, A.D. / ...Authors: Whittamore, P.R. / Addie, M.S. / Bennett, S.N. / Birch, A.M. / Butters, M. / Godfrey, L. / Kenny, P.W. / Morley, A.D. / Murray, P.M. / Oikonomakos, N.G. / Otterbein, L.R. / Pannifer, A.D. / Parker, J.S. / Readman, K. / Siedlecki, P.S. / Schofield, P. / Stocker, A. / Taylor, M.J. / Townsend, L.A. / Whalley, D.P. / Whitehouse, J.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)95,8603
Polymers95,2811
Non-polymers5792
Water8,197455
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7206
Polymers190,5622
Non-polymers1,1584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6950 Å2
ΔGint-42 kcal/mol
Surface area55740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.781, 126.781, 115.144
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-1354-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis:

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 95280.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rabbit muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-3TH / 2-CHLORO-N-[(3R)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE


Mass: 345.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12ClN3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.1mM IMP 1.1mM Spermin 10mM BES 2.9mM DTT 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2001 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.3→91.29 Å / Num. all: 40113 / Num. obs: 39447 / % possible obs: 98.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.54 Å / % possible all: 39.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE MODEL

Resolution: 2.3→91.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.732 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.34 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 2093 5 %RANDOM
Rwork0.18249 ---
all0.18564 40113 --
obs0.18564 39447 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.819 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.3 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6545 0 38 455 7038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226746
X-RAY DIFFRACTIONr_bond_other_d0.0020.026133
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9579132
X-RAY DIFFRACTIONr_angle_other_deg1.14314206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3923.516347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.051151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1331560
X-RAY DIFFRACTIONr_chiral_restr0.090.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021442
X-RAY DIFFRACTIONr_nbd_refined0.2110.21556
X-RAY DIFFRACTIONr_nbd_other0.190.26516
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23197
X-RAY DIFFRACTIONr_nbtor_other0.0890.23925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2424
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.214
X-RAY DIFFRACTIONr_mcbond_it0.9571.55229
X-RAY DIFFRACTIONr_mcbond_other0.1651.51627
X-RAY DIFFRACTIONr_mcangle_it1.14126472
X-RAY DIFFRACTIONr_scbond_it1.88933207
X-RAY DIFFRACTIONr_scangle_it2.7544.52660
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 141 -
Rwork0.194 2719 -
obs--93.22 %
Refinement TLS params.Method: refined / Origin x: 21.1269 Å / Origin y: 98.8218 Å / Origin z: 2.3186 Å
111213212223313233
T-0.0336 Å20.0763 Å2-0.0144 Å2--0.0414 Å2-0.0115 Å2---0.0234 Å2
L0.0962 °2-0.0232 °2-0.0541 °2-0.2002 °2-0.0144 °2--0.4874 °2
S-0.0087 Å °0.0156 Å °-0.0115 Å °-0.0194 Å °-0.0226 Å °0.0025 Å °-0.0263 Å °-0.0574 Å °0.0314 Å °

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