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- PDB-5zj9: human D-amino acid oxidase complexed with 5-chlorothiophene-3-car... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zj9 | |||||||||
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Title | human D-amino acid oxidase complexed with 5-chlorothiophene-3-carboxylic acid | |||||||||
![]() | D-amino-acid oxidase | |||||||||
![]() | OXIDOREDUCTASE / D-amino acid / flavoenzyme | |||||||||
Function / homology | ![]() D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / Peroxisomal protein import / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kato, Y. / Hin, N. / Maita, N. / Thomas, A.G. / Kurosawa, S. / Rojas, C. / Yorita, K. / Slusher, B.S. / Fukui, K. / Tsukamoto, T. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids Authors: Kato, Y. / Hin, N. / Maita, N. / Thomas, A.G. / Kurosawa, S. / Rojas, C. / Yorita, K. / Slusher, B.S. / Fukui, K. / Tsukamoto, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.7 KB | Display | ![]() |
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PDB format | ![]() | 232.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 54.2 KB | Display | |
Data in CIF | ![]() | 70.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zjaC ![]() 2du8S 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38699.910 Da / Num. of mol.: 4 / Fragment: UNP residues 1-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-9E6 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15%(w/v) PEG 4000, 0.2M ammonium acetate, 0.1M Na citrate at pH 8.0, 10%(v/v) glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.15 Å / Num. obs: 44351 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.126 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 1.348 / Num. unique obs: 4577 / CC1/2: 0.731 / Rpim(I) all: 0.741 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2du8 Resolution: 2.6→39.15 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.6→39.15 Å
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