+Open data
-Basic information
Entry | Database: PDB / ID: 8pqo | ||||||
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Title | PITP in complex with the inhibitor VT01545 | ||||||
Components | Phosphatidylinositol transfer protein alpha isoform | ||||||
Keywords | LIPID BINDING PROTEIN / lipid / phosphatidylinositol / Phosphatidylcholine / transfer protein | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Boura, E. / Eisenreichova, A. | ||||||
Funding support | 1items
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Citation | Journal: Embo J. / Year: 2024 Title: Non-vesicular phosphatidylinositol transfer plays critical roles in defining organelle lipid composition. Authors: Kim, Y.J. / Pemberton, J.G. / Eisenreichova, A. / Mandal, A. / Koukalova, A. / Rohilla, P. / Sohn, M. / Konradi, A.W. / Tang, T.T. / Boura, E. / Balla, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pqo.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pqo.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/8pqo ftp://data.pdbj.org/pub/pdb/validation_reports/pq/8pqo | HTTPS FTP |
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-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
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 31838.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PITPNA, PITPN / Production host: Escherichia coli (E. coli) / References: UniProt: Q00169 |
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-Non-polymers , 10 types, 247 molecules
#2: Chemical | ChemComp-IMD / | ||||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-NI / | #5: Chemical | ChemComp-F8O / ( | Mass: 156.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | ChemComp-FDO / ( | Mass: 144.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N2O / Feature type: SUBJECT OF INVESTIGATION #7: Chemical | ChemComp-BU4 / ( | #8: Chemical | ChemComp-MV9 / ( | #9: Chemical | ChemComp-UYA / ( | #10: Chemical | ChemComp-FH6 / ( | Mass: 202.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N2O2S / Feature type: SUBJECT OF INVESTIGATION #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.42 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.95 / Stereochemistry target values: ML
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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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