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Yorodumi- PDB-1em6: HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1em6 | ||||||
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Title | HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-526,423 | ||||||
Components | LIVER GLYCOGEN PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / allosteric site / allosteric binding | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Rath, V.L. / Ammirati, M. / Danley, D.E. / Ekstrom, J.L. / Hynes, T.R. / Olson, T.V. / Hoover, D.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2000 Title: Human liver glycogen phosphorylase inhibitors bind at a new allosteric site. Authors: Rath, V.L. / Ammirati, M. / Danley, D.E. / Ekstrom, J.L. / Gibbs, E.M. / Hynes, T.R. / Mathiowetz, A.M. / McPherson, R.K. / Olson, T.V. / Treadway, J.L. / Hoover, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1em6.cif.gz | 336.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1em6.ent.gz | 272.1 KB | Display | PDB format |
PDBx/mmJSON format | 1em6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1em6 ftp://data.pdbj.org/pub/pdb/validation_reports/em/1em6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 97276.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PBLUEBACII / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06737, glycogen phosphorylase #2: Sugar | |
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-Non-polymers , 4 types, 741 molecules
#3: Chemical | ChemComp-CP4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Apr 18, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 105649 / Num. obs: 103325 / % possible obs: 97.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.359 / Num. unique all: 9224 / % possible all: 87.1 |
Reflection | *PLUS Lowest resolution: 99 Å |
Reflection shell | *PLUS % possible obs: 87.1 % |
-Processing
Software |
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Refinement | Resolution: 2.2→99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 194745.34 / Data cutoff high rms absF: 194745.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS default
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.103 Å2 / ksol: 0.349441 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→99 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.34 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.307 / Rfactor obs: 0.307 |