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Yorodumi- PDB-2bxk: Human serum albumin complexed with myristate, azapropazone and in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bxk | |||||||||
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Title | Human serum albumin complexed with myristate, azapropazone and indomethacin | |||||||||
Components | SERUM ALBUMIN | |||||||||
Keywords | TRANSPORT PROTEIN / ALBUMIN / CARRIER PROTEIN / LIPID-BINDING / METAL-BINDING / DRUG-BINDING / AZAPROPAZONE / MYRISTATE / INDOMETHACIN | |||||||||
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 / nucleus / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Ghuman, J. / Zunszain, P.A. / Petitpas, I. / Bhattacharya, A.A. / Curry, S. | |||||||||
Citation | 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bxk.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bxk.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/2bxk ftp://data.pdbj.org/pub/pdb/validation_reports/bx/2bxk | HTTPS FTP |
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-Related structure data
Related structure data | 2bx8C 2bxaC 2bxbC 2bxcC 2bxdC 2bxeC 2bxfC 2bxgC 2bxhC 2bxiC 2bxlC 2bxmC 2bxnC 2bxoC 2bxpC 2bxqC 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: 66543.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02768 | ||||||||
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#2: Chemical | ChemComp-MYR / #3: Chemical | ChemComp-IMN / | #4: Chemical | ChemComp-AZQ / | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE CONTAINS SIGNAL AND PRO-PEPTIDE (RESIDUES 1-24 IN DATABASE ENTRY). PROTEIN CRYSTALLISED ...SEQUENCE CONTAINS SIGNAL AND PRO-PEPTIDE (RESIDUES 1-24 IN DATABASE ENTRY). PROTEIN CRYSTALLIS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 44 % |
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Crystal grow | pH: 7 / Details: pH 7.00 |
-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: Oct 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→22.3 Å / Num. obs: 25123 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E7G Resolution: 2.4→21.56 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1792393.36 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3534 Å2 / ksol: 0.335879 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→21.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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