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- PDB-4fzb: Structure of thymidylate synthase ThyX complexed to a new inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fzb | ||||||
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Title | Structure of thymidylate synthase ThyX complexed to a new inhibitor | ||||||
![]() | Probable thymidylate synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Homotetramer / FAD-dependent Thymidylate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Basta, T. / Boum, Y. / Briffotaux, J. / Becker, H.F. / Lamarre-Jouenne, I. / Lambry, J.C. / Skouloubris, S. / Liebl, U. / van Tilbeurgh, H. / Graille, M. / Myllylkallio, H. | ||||||
![]() | ![]() Title: Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Authors: Basta, T. / Boum, Y. / Briffotaux, J. / Becker, H.F. / Lamarre-Jouenne, I. / Lambry, J.C. / Skouloubris, S. / Liebl, U. / Graille, M. / van Tilbeurgh, H. / Myllykallio, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 654.1 KB | Display | ![]() |
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PDB format | ![]() | 544.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 8.6 MB | Display | ![]() |
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Full document | ![]() | 8.8 MB | Display | |
Data in XML | ![]() | 126.3 KB | Display | |
Data in CIF | ![]() | 154 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cfaS 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26212.752 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-0VJ / #4: Chemical | ChemComp-DMS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 10% PEG 5000 MME, 12% isopropanol, 12% DMSO, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K PH range: 6,5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→35 Å / Num. all: 120946 / Num. obs: 111996 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.25 % / Biso Wilson estimate: 61.94 Å2 / Rsym value: 0.069 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.59→2.75 Å / Redundancy: 2.25 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.524 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CFA Resolution: 2.59→34.21 Å / Cor.coef. Fo:Fc: 0.9172 / Cor.coef. Fo:Fc free: 0.8805 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 53.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.385 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→34.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.66 Å / Total num. of bins used: 20
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