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- PDB-2ati: Glycogen Phosphorylase Inhibitors -

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Basic information

Entry
Database: PDB / ID: 2ati
TitleGlycogen Phosphorylase Inhibitors
ComponentsGlycogen phosphorylase, liver form
KeywordsTRANSFERASE / Glycogen Phosphorylase
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding / 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
alpha-D-glucopyranose / Chem-IHU / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKlabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.J. / Herling, A.W. / Oikonomakos, N.G. / Schmoll, D. / Sarubbi, E. / von Roedern, E. ...Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.J. / Herling, A.W. / Oikonomakos, N.G. / Schmoll, D. / Sarubbi, E. / von Roedern, E. / Schoenafinger, K. / Defossa, E.
Citation
Journal: J.Med.Chem. / Year: 2005
Title: Acyl ureas as human liver glycogen phosphorylase inhibitors for the treatment of type 2 diabetes.
Authors: Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.J. / Herling, A.W. / Oikonomakos, N.G. / Kosmopoulou, M.N. / Schmoll, D. / Sarubbi, E. / von Roedern, E. / Defossa, E.
#1: Journal: Protein Sci. / Year: 2005
Title: Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs
Authors: Oikonomakos, N.G. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Kostas, I.D. / Wendt, K.U. / Klabunde, T. / Defossa, E.
#2: Journal: Mol.Cell / Year: 2000
Title: Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
Authors: Rath, V.L. / Ammirati, M. / LeMotte, P.K. / Fennell, K.F. / Mansour, M.N. / Danley, D.E. / Hynes, T.R. / Schulte, G.K. / Wasilko, D.J. / Pandit, J.
History
DepositionAug 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
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)195,8238
Polymers194,2912
Non-polymers1,5326
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-26 kcal/mol
Surface area57060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.5, 124.5, 123.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Glycogen phosphorylase, liver form / / liver glycogen phosphorylase A


Mass: 97145.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06737, glycogen phosphorylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-IHU / N-(2-CHLORO-4-FLUOROBENZOYL)-N'-(5-HYDROXY-2-METHOXYPHENYL)UREA / 1-(2-CHLORO-4-FLUORO-BENZOYL)-3-(5-HYDROXY-2-METHOXY-PHENYL)-UREA


Mass: 338.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClFN2O4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.84 Å3/Da / Density % sol: 56.63 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→500 Å / Num. all: 168283 / Num. obs: 167664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameClassification
MOSFLMdata reduction
XDSdata reduction
AMoREphasing
CNXrefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 1.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 8384 -RANDOM
Rwork0.232 ---
all0.234 167664 --
obs0.234 167664 99.6 %-
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12842 0 100 759 13701

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