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Open data
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Basic information
Entry | Database: PDB / ID: 8pqo | ||||||||||||
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Title | PITP in complex with the inhibitor VT01545 | ||||||||||||
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![]() | LIPID BINDING PROTEIN / lipid / phosphatidylinositol / Phosphatidylcholine / transfer protein | ||||||||||||
Function / homology | ![]() phosphatidylcholine transfer activity / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phosphatidylglycerol binding / Role of second messengers in netrin-1 signaling / phosphatidylcholine binding / phospholipid transport / visual perception / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding ...phosphatidylcholine transfer activity / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phosphatidylglycerol binding / Role of second messengers in netrin-1 signaling / phosphatidylcholine binding / phospholipid transport / visual perception / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding / axonogenesis / lipid metabolic process / lipid binding / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Boura, E. / Eisenreichova, A. | ||||||||||||
Funding support | 1items
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![]() | ![]() Title: PITP in complex with the inhibitor VT01545 Authors: Boura, E. / Eisenreichova, 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 | ![]() | 80.6 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
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
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 31941.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 707.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 241 molecules ![](data/chem/img/IMD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IMD / | ||||
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#4: Chemical | #5: Chemical | ChemComp-NI / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Imidazole pH = 8.0, 10% PEG 8 000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25.42 Å / Num. obs: 17995 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 1.364 / Num. unique obs: 1760 / CC1/2: 0.956 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25.42 Å
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Refine LS restraints |
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LS refinement shell |
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