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Yorodumi- PDB-5ae1: Ether Lipid-Generating Enzyme AGPS in complex with inhibitor ZINC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ae1 | ||||||
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Title | Ether Lipid-Generating Enzyme AGPS in complex with inhibitor ZINC69435460 | ||||||
Components | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL | ||||||
Keywords | TRANSFERASE / ETHER PHOSPHOLIPID / CANCER / FLAVIN | ||||||
Function / homology | Function and homology information alkylglycerone-phosphate synthase / alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / peroxisomal membrane / FAD binding / peroxisome Similarity search - Function | ||||||
Biological species | CAVIA PORCELLUS (domestic guinea pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Piano, V. / Benjamin, D.I. / Valente, S. / Nenci, S. / Marrocco, B. / Mai, A. / Aliverti, A. / Nomura, D.K. / Mattevi, A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Discovery of Inhibitors for the Ether Lipid-Generating Enzyme Agps as Anti-Cancer Agents. Authors: Piano, V. / Benjamin, D.I. / Valente, S. / Nenci, S. / Marrocco, B. / Mai, A. / Aliverti, A. / Nomura, D.K. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ae1.cif.gz | 456 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ae1.ent.gz | 372.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ae1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ae1_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5ae1_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5ae1_validation.xml.gz | 83.7 KB | Display | |
Data in CIF | 5ae1_validation.cif.gz | 114.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5ae1 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5ae1 | HTTPS FTP |
-Related structure data
Related structure data | 5adzC 5ae2C 5ae3C 4bbyS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 72938.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAVIA PORCELLUS (domestic guinea pig) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P97275, alkylglycerone-phosphate synthase #2: Chemical | ChemComp-B2Z / ( #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.03 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: PEG 1500 20% HEPES 100 MM PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.14 Å / Num. obs: 135947 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.8 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BBY Resolution: 2.1→107.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.962 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 32.446 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→107.01 Å
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Refine LS restraints |
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