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Yorodumi- PDB-1hk5: HUMAN SERUM ALBUMIN MUTANT R218H COMPLEXED WITH THYROXINE (3,3',5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hk5 | |||||||||
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Title | HUMAN SERUM ALBUMIN MUTANT R218H COMPLEXED WITH THYROXINE (3,3',5,5'-TETRAIODO-L-THYRONINE) and myristic acid (tetradecanoic acid) | |||||||||
Components | SERUM ALBUMIN | |||||||||
Keywords | PLASMA PROTEIN / HORMONE-BINDING / LIPID-BINDING / THYROXINE / FAMILIAL DYSALBUMINEMIC HYPERTHYROXINEMIA | |||||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Petitpas, I. / Petersen, C.E. / Ha, C.E. / Bhattacharya, A.A. / Zunszain, P.A. / Ghuman, J. / Bhagavan, N.V. / Curry, S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Structural Basis of Albumin-Thyroxine Interactions and Familial Dysalbuminemic Hyperthyroxinemia Authors: Petitpas, I. / Petersen, C.E. / Ha, C.E. / Bhattacharya, A.A. / Zunszain, P.A. / Ghuman, J. / Bhagavan, N.V. / Curry, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hk5.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hk5.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hk5 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hk5 | HTTPS FTP |
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-Related structure data
Related structure data | 1hk1C 1hk2C 1hk3C 1hk4C 1e7gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66552.172 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02768 | ||||||
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#2: Chemical | ChemComp-MYR / #3: Chemical | ChemComp-T44 / | #4: Water | ChemComp-HOH / | Compound details | SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE OF WATER, IT BINDS TO CA++, NA+, K+, FATTY ...SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE OF WATER, IT BINDS TO CA++, NA+, K+, FATTY ACIDS, HORMONES, BILIRUBIN AND DRUGS ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % | ||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.6 Å / Num. obs: 17211 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.8 / % possible all: 80 |
Reflection shell | *PLUS % possible obs: 80 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E7G Resolution: 2.7→38.19 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1758838 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED RESIDUES 1-2 AND 585 ARE DISORDERED AND HAVE NOT BEEN INCLUDED IN THE MODEL.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.8694 Å2 / ksol: 0.316545 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→38.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 46.6 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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