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Yorodumi- PDB-1hk3: Human serum albumin mutant r218p complexed with thyroxine (3,3',5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hk3 | |||||||||
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Title | Human serum albumin mutant r218p complexed with thyroxine (3,3',5,5'-tetraiodo-l-thyronine) | |||||||||
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 / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / 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: 2.8 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 | 1hk3.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hk3.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hk3 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hk3 | HTTPS FTP |
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-Related structure data
Related structure data | 1hk1C 1hk2C 1hk4C 1hk5C 1e7aS 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: 66511.141 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-T44 / #3: 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8019 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8019 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35.4 Å / Num. obs: 14600 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 97.7 |
Reflection | *PLUS % possible obs: 85.1 % / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E7A Resolution: 2.8→35.12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1111306.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.869 Å2 / ksol: 0.262542 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→35.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / 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: 35.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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