[English] 日本語
Yorodumi- PDB-1ww2: Crystallographic studies on two bioisosteric analogues, N-acetyl-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ww2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoroacetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / glycogenolysis / type 2 diabetes | ||||||
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 | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Anagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Hadjiloi, T. / Tiraidis, C. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. ...Anagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Hadjiloi, T. / Tiraidis, C. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. / Gergely, P. / Kolisis, F.N. / Oikonomakos, N.G. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2006 Title: Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-d-glucopyranosylamine and N-trifluoroacetyl-beta-d-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase Authors: Anagnostou, E. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Hadjiloi, T. / Tiraidis, C. / Zographos, S.E. / Gyorgydeak, Z. / Somsak, L. / Docsa, T. / Gergely, P. / Kolisis, F.N. / Oikonomakos, N.G. #1: Journal: Protein Sci. / Year: 1995 Title: N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R. #2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1995 Title: Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection Authors: Watson, K.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ww2.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ww2.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ww2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/1ww2 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/1ww2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ww3C 2prjS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Dimeric glycogen phosphorylase is the physiologiacally active species |
-Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MuscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
---|---|
#2: Sugar | ChemComp-NBG / |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.91 % |
---|---|
Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10mM Bes buffer, 3mM DDT, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.36 Å / Num. obs: 68661 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3387 / % possible all: 89.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2PRJ Resolution: 1.9→29.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3297897 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1731 Å2 / ksol: 0.311396 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.36 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|