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- PDB-6dnd: Crystal structure of wild-type (WT) human Glutamate oxaloacetate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dnd | ||||||
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Title | Crystal structure of wild-type (WT) human Glutamate oxaloacetate transaminase 1 (GOT1) | ||||||
![]() | Aspartate aminotransferase, cytoplasmic![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 175.1 KB | Display | ![]() |
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PDB format | ![]() | 138.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dnaC ![]() 6dnbC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 3 - 410 / Label seq-ID: 1 - 408
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Components
#1: Protein | ![]() Mass: 46097.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P17174, ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Acetate Trihydrate pH 4.5, 25% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→50 Å / Num. obs: 3512 / % possible obs: 99.92 % / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.01 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.32 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3ii0 Resolution: 2.1→68.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.27 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.212 / 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 | Biso mean: 57.577 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→68.85 Å
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Refine LS restraints |
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