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Open data
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Basic information
Entry | Database: PDB / ID: 1fa9 | ||||||
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Title | HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH AMP | ||||||
![]() | GLYCOGEN PHOSPHORYLASE, LIVER FORM | ||||||
![]() | TRANSFERASE / protein-ligand complex / allosteric protein / phosphorylated protein | ||||||
Function / homology | ![]() vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-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 / D-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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.8 KB | Display | ![]() |
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PDB format | ![]() | 146.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.3 KB | Display | ![]() |
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Full document | ![]() | 865.7 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 51.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fc0C ![]() 1gpaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold. |
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Components
#1: Protein | Mass: 97225.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-AMP / |
#4: Chemical | ChemComp-PLP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Peg 8000, Tris/HCl, AMP, glucose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 19, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 44772 / Num. obs: 43732 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 9 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.495 / % possible all: 91.8 |
Reflection | *PLUS Num. obs: 53400 |
Reflection shell | *PLUS % possible obs: 91.8 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1GPA Resolution: 2.4→50 Å / Cross valid method: X-PLOR / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å / Rfactor Rfree: 0.476 / Rfactor Rwork: 0.353 | |||||||||||||||||||||||||
Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å / Rfactor Rfree: 0.476 / Rfactor Rwork: 0.353 / Rfactor obs: 0.353 |