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- PDB-3cem: Human glycogen phosphorylase (tense state) in complex with the al... -

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Basic information

Entry
Database: PDB / ID: 3cem
TitleHuman glycogen phosphorylase (tense state) in complex with the allosteric inhibitor AVE9423
ComponentsGlycogen phosphorylase, liver form
KeywordsTRANSFERASE / protein ligand complex / tense state / allosteric inhibitor / Allosteric enzyme / Carbohydrate metabolism / Disease mutation / Glycogen metabolism / Glycogen storage disease / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / bile acid binding / glycogen catabolic process ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / bile acid binding / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
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-AVD / N-acetyl-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsWendt, K.U. / Dreyer, M.K. / Anderka, O. / Klabunde, T. / Loenze, P. / Defossa, E. / Schmoll, D.
CitationJournal: Biochemistry / Year: 2008
Title: Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors.
Authors: Anderka, O. / Loenze, P. / Klabunde, T. / Dreyer, M.K. / Defossa, E. / Wendt, K.U. / Schmoll, D.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 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 / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, liver form
B: Glycogen phosphorylase, liver form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,0748
Polymers186,1272
Non-polymers1,9476
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-16.9 kcal/mol
Surface area56140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.383, 124.383, 123.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Glycogen phosphorylase, liver form


Mass: 93063.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYGL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06737, glycogen phosphorylase
#2: Sugar ChemComp-NBG / N-acetyl-beta-D-glucopyranosylamine


Type: D-saccharide / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
b-D-Glcp1NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-AVD / 1-(2-carboxyphenyl)-7-chloro-6-[(2-chloro-4,6-difluorophenyl)amino]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid


Mass: 505.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H12Cl2F2N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 7 mg/ml in 20 mM BES, 1 mM EDTA, 0.5 mM DTT, pH 6.5, 50 mM NBG, 2.5 mM AVD (AVE9423), VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.47→49.39 Å / Num. obs: 76587 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.47→49.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.119 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 5343 7 %RANDOM
Rwork0.155 ---
obs0.159 76582 99.95 %-
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: 35.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.47→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12898 0 130 501 13529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02213370
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.96818103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06951590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76124.275648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.454152377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641580
X-RAY DIFFRACTIONr_chiral_restr0.1270.21966
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210128
X-RAY DIFFRACTIONr_nbd_refined0.230.26501
X-RAY DIFFRACTIONr_nbtor_refined0.3220.29090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2779
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.211
X-RAY DIFFRACTIONr_mcbond_it1.0811.58179
X-RAY DIFFRACTIONr_mcangle_it1.809212846
X-RAY DIFFRACTIONr_scbond_it2.85636031
X-RAY DIFFRACTIONr_scangle_it4.4464.55257
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 378 -
Rwork0.214 5322 -
all-5700 -
obs--100 %

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