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- PDB-9eo8: X-ray structure of the adduct formed upon reaction of picoplatin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9eo8 | ||||||
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Title | X-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure D) | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | RNA BINDING PROTEIN / picoplatin / lysozyme / protein / interaction | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Picoplatin binding to proteins: X-ray structures and mass spectrometry data on the adducts with lysozyme and ribonuclease A. Authors: Ferraro, G. / Lyckova, T. / Massai, L. / Starha, P. / Messori, L. / Merlino, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9enzC ![]() 9eo2C ![]() 9eo5C 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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2 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 215 molecules ![](data/chem/img/NH3.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NH3 / #3: Chemical | ChemComp-PT / #4: Chemical | ChemComp-CL / #5: Chemical | Mass: 339.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9ClN2Pt / Feature type: SUBJECT OF INVESTIGATION #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4000, 0.1 M sodium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→28.83 Å / Num. obs: 24352 / % possible obs: 98.3 % / Redundancy: 6.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.76→1.81 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1413 / CC1/2: 0.792 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→28.83 Å
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Refine LS restraints |
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LS refinement shell |
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