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- PDB-5lqn: Crystal Structure of COMT in complex with 2-[(3-chlorophenoxy)met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lqn | ||||||
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Title | Crystal Structure of COMT in complex with 2-[(3-chlorophenoxy)methyl]-4-methyl-5-(1H-pyrazol-5-yl)-1,3-thiazole | ||||||
![]() | Catechol O-methyltransferase![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ehler, A. / Lerner, C. / Rudolph, M.G. | ||||||
![]() | ![]() Title: Crystal Structure of COMT in complex with 2-[(3-chlorophenoxy)methyl]-4-methyl-5-(1H-pyrazol-5-yl)-1,3-thiazole Authors: Lerner, C. / Rudolph, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.3 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-72O / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→47.65 Å / Num. obs: 24349 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 39.176 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.51 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: inhouse model Resolution: 1.72→47.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.144 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 Details: 3-Chloro-phenoxymethyl not well defined by electron density; could be mixture of 2-(3-Chloro-phenoxymethyl)-4-methyl-5-(2H-pyrazol-3-yl)-thiazole and molecule derived from starting material, ...Details: 3-Chloro-phenoxymethyl not well defined by electron density; could be mixture of 2-(3-Chloro-phenoxymethyl)-4-methyl-5-(2H-pyrazol-3-yl)-thiazole and molecule derived from starting material, e.g. 4-methyl-5-(2H-pyrazol-3-yl)-thiazole. orientation of chloro-substituent rather certain.
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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 max: 80 Å2 / Biso mean: 36.19 Å2 / Biso min: 27.22 Å2
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Refinement step | Cycle: final / Resolution: 1.72→47.65 Å
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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