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Yorodumi- PDB-6v8d: Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v8d | ||||||
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Title | Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators | ||||||
Components | Ornithine aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / Human Ornithine Aminotransferase (hOAT) / Mechanism Based Inactivator / PLP Hepatocellular Carcinoma (HCC) | ||||||
Function / homology | Function and homology information arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Zhu, W. / Doubleday, P.T. / Catlin, D.S. / Weerawarna, P. / Butrin, A. / Shen, S. / Kelleher, N.L. / Liu, D. / Silverman, R.B. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators Authors: Zhu, W. / Doubleday, P.T. / Catlin, D.S. / Weerawarna, P. / Butrin, A. / Shen, S. / Kelleher, N.L. / Liu, D. / Silverman, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v8d.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v8d.ent.gz | 203.3 KB | Display | PDB format |
PDBx/mmJSON format | 6v8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v8d_validation.pdf.gz | 502.2 KB | Display | wwPDB validaton report |
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Full document | 6v8d_full_validation.pdf.gz | 504.6 KB | Display | |
Data in XML | 6v8d_validation.xml.gz | 1.9 KB | Display | |
Data in CIF | 6v8d_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8d ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8d | HTTPS FTP |
-Related structure data
Related structure data | 6v8cC 1oatS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44860.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 16.5% PEG 1000 240 mM NaCl 25% glycerol 50 mM Tricine pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→32 Å / Num. obs: 54461 / % possible obs: 91.73 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.25→2.33 Å / Num. unique obs: 3671 / CC1/2: 0.891 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OAT Resolution: 2.25→31.36 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.04 Å2 / Biso mean: 29.9815 Å2 / Biso min: 14.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→31.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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