+Open data
-Basic information
Entry | Database: PDB / ID: 3tdl | ||||||
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Title | Structure of human serum albumin in complex with DAUDA | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / PROTEIN-DRUG COMPLEX / Human serum albumin / Myristate / DAUDA / fluorescent fatty acid analogue / protein binding | ||||||
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: 2.6 Å | ||||||
Authors | Wang, Y. / Luo, Z. / Shi, X. / Wang, H. / Nie, L. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: A fluorescent fatty acid probe, DAUDA, selectively displaces two myristates bound in human serum albumin Authors: Wang, Y. / Luo, Z. / Shi, X. / Wang, H. / Nie, L. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tdl.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tdl.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/3tdl ftp://data.pdbj.org/pub/pdb/validation_reports/td/3tdl | HTTPS FTP |
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-Related structure data
Related structure data | 1bj5S S: Starting model for refinement |
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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: 66571.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 Production host: Pichia pastoris (fungus) / References: UniProt: P02768 | ||
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#2: Chemical | ChemComp-MYR / #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 28-32% (w/v) polyethylene glycol 3350, 50mM potassium phosphate (pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.04 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99 Å / Num. obs: 17658 / Biso Wilson estimate: 48.2 Å2 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BJ5 Resolution: 2.6→35.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1984703.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.7034 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→35.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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