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Open data
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Basic information
Entry | Database: PDB / ID: 5adz | ||||||
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Title | Ether Lipid-Generating Enzyme AGPS in complex with inhibitor 1a | ||||||
![]() | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL | ||||||
![]() | TRANSFERASE / ETHER PHOSPHOLIPID / CANCER / FLAVIN | ||||||
Function / homology | ![]() alkylglycerone-phosphate synthase / alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / peroxisomal membrane / FAD binding / peroxisome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Piano, V. / Benjamin, D.I. / Valente, S. / Nenci, S. / Marrocco, B. / Mai, A. / Aliverti, A. / Nomura, D.K. / Mattevi, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 457.6 KB | Display | ![]() |
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PDB format | ![]() | 374.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 84.1 KB | Display | |
Data in CIF | ![]() | 116 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ae1C ![]() 5ae2C ![]() 5ae3C ![]() 4bbyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P97275, alkylglycerone-phosphate synthase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-KQS / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.16 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: PEG 1500 20%, HEPES, PH 7.5, 100 MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32 Å / Num. obs: 117589 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BBY Resolution: 2.2→107.96 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.952 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→107.96 Å
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Refine LS restraints |
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