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- PDB-6dnb: Crystal structure of T110A:S256A mutant human Glutamate oxaloacet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dnb | ||||||
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Title | Crystal structure of T110A:S256A mutant human Glutamate oxaloacetate transaminase 1 (GOT1) | ||||||
![]() | Aspartate aminotransferase, cytoplasmic | ||||||
![]() | TRANSFERASE / Aspartate aminotransferase / Glutamate oxaloacetate transaminase 1 / GOT1 / PLP | ||||||
Function / homology | ![]() phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / glycerol biosynthetic process / aspartate metabolic process / aspartate biosynthetic process / Aspartate and asparagine metabolism ...phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / glycerol biosynthetic process / aspartate metabolic process / aspartate biosynthetic process / Aspartate and asparagine metabolism / glutamate metabolic process / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / Gluconeogenesis / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Assar, Z. / Holt, M.C. / Stein, A.J. / Lairson, L. / Lyssiotis, C.A. | ||||||
![]() | ![]() Title: Biochemical Characterization and Structure-Based Mutational Analysis Provide Insight into the Binding and Mechanism of Action of Novel Aspartate Aminotransferase Inhibitors. Authors: Holt, M.C. / Assar, Z. / Beheshti Zavareh, R. / Lin, L. / Anglin, J. / Mashadova, O. / Haldar, D. / Mullarky, E. / Kremer, D.M. / Cantley, L.C. / Kimmelman, A.C. / Stein, A.J. / Lairson, L.L. / Lyssiotis, C.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 | ![]() | 103.7 KB | Display | ![]() |
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PDB format | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dnaC ![]() 6dndC ![]() 3ii0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46050.066 Da / Num. of mol.: 1 / Mutation: T110A, S256A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17174, aspartate transaminase, cysteine transaminase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 20% w/v/ PEG MME 2,000, 0.2 M Trimethylamine N-oxide dehydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 46568 / % possible obs: 99.76 % / Redundancy: 14.24 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 47.62 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 0.51 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ii0 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.242 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.111 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.887 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50 Å
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Refine LS restraints |
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