[English] 日本語
Yorodumi- PDB-1pyg: STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pyg | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE | ||||||
Components | GLYCOGEN PHOSPHORYLASE B | ||||||
Keywords | 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 | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.87 Å | ||||||
Authors | Sprang, S. | ||||||
Citation | Journal: Science / Year: 1991 Title: Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate. Authors: Sprang, S.R. / Withers, S.G. / Goldsmith, E.J. / Fletterick, R.J. / Madsen, N.B. #1: Journal: Protein Sci. / Year: 1992 Title: Multiple Phosphate Positions in the Catalytic Site of Glycogen Phosphorylase: Structure of the Pyridoxal-5'-Pyrophosphate Coenzyme-Substrate Analog Authors: Sprang, S.R. / Madsen, N.B. / Withers, S.G. #2: Journal: Science / Year: 1989 Title: Domain Separation in the Activation of Glycogen Phosphorylase A Authors: Goldsmith, E.J. / Sprang, S.R. / Hamlin, R. / Xuong, N.-H. / Fletterick, R.J. #3: Journal: Nature / Year: 1988 Title: Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation Authors: Sprang, S.R. / Acharya, K.R. / Goldsmith, E.J. / Stuart, D.I. / Varvill, K. / Fletterick, R.J. / Madsen, N.B. / Johnson, L.N. #4: Journal: Science / Year: 1987 Title: Structure of the Nucleotide Activation Switch in Glycogen Phosphorylase A Authors: Sprang, S. / Goldsmith, E. / Fletterick, R. #5: Journal: Biochemistry / Year: 1982 Title: Catalytic Site of Glycogen Phosphorylase: Structural Changes During Activation and Mechanistic Implications Authors: Withers, S.G. / Madsen, N.B. / Sprang, S.R. / Fletterick, R.J. #6: Journal: J.Biol.Chem. / Year: 1981 Title: Evidence for Direct Phosphate-Phosphate Interaction between Pyridoxal Phosphate and Substrate in the Glycogen Phosphorylase Catalytic Mechanism Authors: Withers, S.G. / Madsen, N.B. / Sykes, B.D. / Takagi, M. / Shimomura, S. / Fukui, T. #7: Journal: J.Mol.Biol. / Year: 1979 Title: The Structure of Glycogen Phosphorylase a at 2.5 Angstroms Resolution Authors: Sprang, S. / Fletterick, R.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pyg.cif.gz | 635 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pyg.ent.gz | 533.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/1pyg ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyg | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Atom site foot note | 1: LEU B 834 - PRO B 835 OMEGA =149.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||
Details | THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *A*. |
-Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-PDP / Compound details | PLPP-GPB IS STABILIZED IN THE CATALYTICALLY ACTIVE R-STATE BY ADENOSINE MONOPHOSPHATE. IN THE ...PLPP-GPB IS STABILIZED | Nonpolymer details | PYRIDOXAL-5'-PYROPHOSPHORYL GLYCOGEN PHOSPHORYLASE B (PLPP-GPB) IS A COVALENT ANALOG OF THE ENZYME- ...PYRIDOXAL-5'-PYROPHOSPH | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Num. all: 88004 / Num. obs: 77728 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Num. measured all: 522198 / Rmerge(I) obs: 0.053 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.87→8 Å / Rfactor Rwork: 0.185 / Rfactor all: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 8 Å / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.2 |