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- PDB-5zja: human D-amino acid oxidase complexed with 5-chlorothiophene-2-car... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zja | ||||||
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Title | human D-amino acid oxidase complexed with 5-chlorothiophene-2-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. | ||||||
![]() | ![]() 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 | ![]() | 553.6 KB | Display | ![]() |
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PDB format | ![]() | 458.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 56.7 KB | Display | |
Data in CIF | ![]() | 72.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zj9C ![]() 2du8S 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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Components
#1: Protein | Mass: 38699.910 Da / Num. of mol.: 4 / Fragment: UNP residues 1-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-9E9 / #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: 45.65 % |
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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, and 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→49.23 Å / Num. obs: 44404 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.108 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 1.786 / Num. unique obs: 4593 / CC1/2: 0.517 / Rpim(I) all: 0.983 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2du8 Resolution: 2.6→49.229 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→49.229 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 123.8747 Å / Origin y: 50.0923 Å / Origin z: 38.4576 Å
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Refinement TLS group | Selection details: all |