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Yorodumi- PDB-3b9m: Human serum albumin complexed with myristate, 3'-azido-3'-deoxyth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b9m | ||||||
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Title | Human serum albumin complexed with myristate, 3'-azido-3'-deoxythymidine (AZT) and salicylic acid | ||||||
Components | Serum albumin | ||||||
Keywords | LIPID BINDING PROTEIN / protein-ligands complex / Cleavage on pair of basic residues / Disease mutation / Glycation / Glycoprotein / Lipid-binding / Metal-binding / Secreted | ||||||
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 | Zhu, L. / Yang, F. / Chen, L. / Meehan, E.J. / Huang, M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2008 Title: A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography Authors: Zhu, L. / Yang, F. / Chen, L. / Meehan, E.J. / Huang, M. #1: Journal: J.Mol.Biol. / Year: 2005 Title: Structural basis of the drug-binding specificity of human serum albumin Authors: Ghuman, J. / Zunszain, P.A. / Petitpas, I. / Bhattacharya, A.A. / Otagiri, M. / Curry, S. #2: Journal: J.Struct.Biol. / Year: 2007 Title: Effect of human serum albumin on drug metabolism: structural evidence of esterase activity of human serum albumin Authors: Yang, F. / Bian, C. / Zhu, L. / Zhao, G. / Huang, Z. / Huang, M. #3: Journal: Nature / Year: 1992 Title: Atomic structure and chemistry of human serum albumin Authors: He, X.M. / Carter, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b9m.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9m.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9m ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9m | HTTPS FTP |
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-Related structure data
Related structure data | 3b9lC 1e7gS C: citing same article (ref.) 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768 | ||||
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#2: Chemical | ChemComp-MYR / #3: Chemical | ChemComp-AZZ / | #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 32%(w/v) polyethylene glycol 3350, 50mM potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID |
Detector | Detector: CCD / Date: Aug 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→55 Å / Num. all: 15958 / Num. obs: 15958 / % possible obs: 54 % / Redundancy: 6 % / Biso Wilson estimate: 8 Å2 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E7G Resolution: 2.7→46.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2355803 / 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: 33.618 Å2 / ksol: 0.315 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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