+Open data
-Basic information
Entry | Database: PDB / ID: 4s1y | ||||||
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Title | X-ray structure of human serum albumin complexed with cisplatin | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / Albumin / drug transport / fatty acids | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.16 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2015 Title: Cisplatin binding to human serum albumin: a structural study. Authors: Ferraro, G. / Massai, L. / Messori, L. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s1y.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s1y.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 4s1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4s1y_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 4s1y_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 4s1y_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4s1y_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/4s1y ftp://data.pdbj.org/pub/pdb/validation_reports/s1/4s1y | HTTPS FTP |
-Related structure data
Related structure data | 1hk1S 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 References: UniProt: P02768 | ||
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#2: Chemical | ChemComp-CPT / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Crystals of a cisplatin/HSA adduct were obtained by soaking: more in detail, crystals of defatted HSA, grown after four weeks by sitting drop vapour diffusion method at 25 C using a ...Details: Crystals of a cisplatin/HSA adduct were obtained by soaking: more in detail, crystals of defatted HSA, grown after four weeks by sitting drop vapour diffusion method at 25 C using a reservoir solution of 30 % w/v polyethylene glycol 3350 in 50 mM potassium phosphate at pH 7.4 and protein concentration of 30 mg mL-1 (see experimental section or further details), were soaked for 24 h in a 0.005 M cisplatin solution in the same reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.16→57.46 Å / Num. all: 9393 / Num. obs: 9393 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.149 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1HK1 Resolution: 3.16→57.46 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.759 / SU B: 36.56 / SU ML: 0.616 / Cross valid method: THROUGHOUT / ESU R Free: 0.737 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 49.033 Å2
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Refinement step | Cycle: LAST / Resolution: 3.16→57.46 Å
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