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Yorodumi- PDB-6lig: Crystal structure of human Glutamate oxaloacetate transaminase 1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lig | ||||||
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Title | Crystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1) in complex with AH | ||||||
Components | Glutamate oxaloacetate transaminase 1 | ||||||
Keywords | TRANSFERASE / inhibitor | ||||||
Function / homology | Function and homology information Malate-aspartate shuttle / 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 catabolic process / aspartate biosynthetic process ...Malate-aspartate shuttle / 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 catabolic process / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / Aspartate and asparagine metabolism / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Yan, S. / Sun, W.G. / Zhang, Y.H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1) in complex with AH Authors: Shan, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lig.cif.gz | 324.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lig.ent.gz | 262.1 KB | Display | PDB format |
PDBx/mmJSON format | 6lig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lig_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6lig_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6lig_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 6lig_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/6lig ftp://data.pdbj.org/pub/pdb/validation_reports/li/6lig | HTTPS FTP |
-Related structure data
Related structure data | 6dndS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Homo sapiens (human) / Gene: GOT1 / Production host: Escherichia coli (E. coli) References: UniProt: P17174, aspartate transaminase, cysteine transaminase #2: Chemical | ChemComp-EE6 / | #3: Chemical | ChemComp-PLP / | #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: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→64.8553 Å / Num. obs: 25267 / % possible obs: 97.67 % / Redundancy: 2 % / CC1/2: 0.989 / Net I/σ(I): 9.34 |
Reflection shell | Resolution: 2.62→2.714 Å / Num. unique obs: 2557 / CC1/2: 0.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DND Resolution: 2.62→64.835 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.46 Å2 / Biso mean: 29.9613 Å2 / Biso min: 8.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→64.835 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -19.6561 Å / Origin y: 2.458 Å / Origin z: -28.1362 Å
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Refinement TLS group |
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