+Open data
-Basic information
Entry | Database: PDB / ID: 8ism | ||||||
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Title | HSA-Pt compound complex | ||||||
Components | Serum albumin | ||||||
Keywords | METAL BINDING PROTEIN / Complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Zhang, J.Z. / Zhang, Z.L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: HSA-Pt compound complex Authors: Zhang, J.Z. / Zhang, Z.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ism.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ism.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ism.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ism_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ism_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ism_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 8ism_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/8ism ftp://data.pdbj.org/pub/pdb/validation_reports/is/8ism | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66214.844 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 kudriavzevii (yeast) / References: UniProt: P02768 | ||||
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#2: Chemical | ChemComp-PLM / #3: Chemical | ChemComp-ZJZ / | Mass: 498.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN4PtS / Feature type: SUBJECT OF INVESTIGATION Has ligand of interest | Y | |
-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: 51.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, 4% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 22, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.3→92.67 Å / Num. obs: 108443 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.249 / Net I/σ(I): 1.38 | ||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→92.67 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.255 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / 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: 82.949 Å2
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Refinement step | Cycle: 1 / Resolution: 2.76→92.67 Å
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