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- PDB-7woj: Crystal structure of HSA-Myr complex soaked with cisplatin for on... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7woj | ||||||
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Title | Crystal structure of HSA-Myr complex soaked with cisplatin for one week | ||||||
![]() | Albumin | ||||||
![]() | TRANSPORT PROTEIN / Human serum albumin / Fatty acid / Cisplatin | ||||||
Function / homology | ![]() 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 / small molecule 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, S.L. / Yuan, C. / Jiang, L.G. / Luo, Z.P. / Huang, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic analysis of interaction between cisplatin and human serum albumin: Effect of fatty acid. Authors: Chen, S.L. / Yuan, C. / Jiang, L.G. / Luo, Z.P. / Huang, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 97.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wokC ![]() 3tdlS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 69469.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 Production host: ![]() | ||||
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#2: Chemical | ChemComp-CPT / #3: Chemical | ChemComp-MYR / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 26-32% PEG 3350, 50mM PB at pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→50 Å / Num. obs: 12296 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.156 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.89→3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 4.652 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1202 / CC1/2: 0.254 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TDL Resolution: 2.89→43.41 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.903 / SU B: 21.732 / SU ML: 0.427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.581 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 235.21 Å2 / Biso mean: 87.872 Å2 / Biso min: 36.47 Å2
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Refinement step | Cycle: final / Resolution: 2.89→43.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.891→2.966 Å / Total num. of bins used: 20
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