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Yorodumi- PDB-1l5s: Human liver glycogen phosphorylase complexed with uric acid, N-Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l5s | ||||||
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Title | Human liver glycogen phosphorylase complexed with uric acid, N-Acetyl-beta-D-glucopyranosylamine, and CP-403,700 | ||||||
Components | Glycogen phosphorylase, liver form | ||||||
Keywords | TRANSFERASE / phosphorylase / purine site | ||||||
Function / homology | Function and homology information 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 / glucose homeostasis / pyridoxal phosphate binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ekstrom, J.L. / Pauly, T.A. / Carty, M.D. / Soeller, W.C. / Culp, J. / Danley, D.E. / Hoover, D.J. / Treadway, J.L. / Gibbs, E.M. / Fletterick, R.J. ...Ekstrom, J.L. / Pauly, T.A. / Carty, M.D. / Soeller, W.C. / Culp, J. / Danley, D.E. / Hoover, D.J. / Treadway, J.L. / Gibbs, E.M. / Fletterick, R.J. / Day, Y.S.N. / Myszka, D.G. / Rath, V.L. | ||||||
Citation | Journal: Chem.Biol. / Year: 2002 Title: Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase. Authors: Ekstrom, J.L. / Pauly, T.A. / Carty, M.D. / Soeller, W.C. / Culp, J. / Danley, D.E. / Hoover, D.J. / Treadway, J.L. / Gibbs, E.M. / Fletterick, R.J. / Day, Y.S. / Myszka, D.G. / Rath, V.L. | ||||||
History |
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Remark 999 | SEQUENCE THE NUMBERING OF THE SEQUENCE IS SHIFTED BY ONE IN AGREEMENT WITH THE CONVENTION IN THE ... SEQUENCE THE NUMBERING OF THE SEQUENCE IS SHIFTED BY ONE IN AGREEMENT WITH THE CONVENTION IN THE LITERATURE FOR THIS PROTEIN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l5s.cif.gz | 345 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l5s.ent.gz | 280.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l5s_validation.pdf.gz | 585.7 KB | Display | wwPDB validaton report |
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Full document | 1l5s_full_validation.pdf.gz | 622.6 KB | Display | |
Data in XML | 1l5s_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 1l5s_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/1l5s ftp://data.pdbj.org/pub/pdb/validation_reports/l5/1l5s | HTTPS FTP |
-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 / Production host: Escherichia coli (E. coli) / References: UniProt: P06737, glycogen phosphorylase #2: Sugar | |
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-Non-polymers , 5 types, 796 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MRD / ( #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % | ||||||||||||||||||||||||||||||||||||||||||
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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 Temperature: 17 ℃ / 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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å |
Detector | Type: BRANDEIS - B1.2 / Detector: CCD / Date: Jun 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99 Å / Num. all: 243830 / Num. obs: 231395 / % possible obs: 94.9 % / Observed criterion σ(I): -2 / Redundancy: 2 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 9378 / Rsym value: 0.417 / % possible all: 75.5 |
Reflection | *PLUS Lowest resolution: 99 Å / Num. obs: 117831 / Num. measured all: 243830 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 75.5 % / Rmerge(I) obs: 0.417 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.6 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 162096.35 / Data cutoff high rms absF: 162096.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.404 Å2 / ksol: 0.326823 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→40.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 75 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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