+Open data
-Basic information
Entry | Database: PDB / ID: 6qa7 | ||||||
---|---|---|---|---|---|---|---|
Title | Glycogen Phosphorylase b in complex with 29 | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.36 Å | ||||||
Authors | Kyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography. Authors: Szabo, K.E. / Kyriakis, E. / Psarra, A.G. / Karra, A.G. / Sipos, A. / Docsa, T. / Stravodimos, G.A. / Katsidou, E. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Mandi, A. / Kiraly, S. ...Authors: Szabo, K.E. / Kyriakis, E. / Psarra, A.G. / Karra, A.G. / Sipos, A. / Docsa, T. / Stravodimos, G.A. / Katsidou, E. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Mandi, A. / Kiraly, S.B. / Kurtan, T. / Leonidas, D.D. / Somsak, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qa7.cif.gz | 335.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qa7.ent.gz | 282.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qa7 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qa7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 97422.398 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: Chemical | ChemComp-HTW / ( |
#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: 2.45 Å3/Da / Density % sol: 49.7 % |
---|---|
Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5419 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: May 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→13.7 Å / Num. obs: 35956 / % possible obs: 90.2 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rsym value: 0.08 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.36→2.45 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3168 / CC1/2: 0.859 / Rsym value: 0.583 / % possible all: 76.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.36→13.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.835 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.915 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.36→13.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|