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- PDB-1nmy: Crystal structure of human thymidylate kinase with FLTMP and AppNHp -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nmy | ||||||
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Title | Crystal structure of human thymidylate kinase with FLTMP and AppNHp | ||||||
![]() | similar to THYMIDYLATE KINASE (DTMP KINASE) | ||||||
![]() | TRANSFERASE / thymidylate kinase / p-loop / fluorothymidine | ||||||
Function / homology | ![]() thymidine biosynthetic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / myoblast differentiation / nucleoside diphosphate kinase activity / dTTP biosynthetic process / response to cadmium ion ...thymidine biosynthetic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / myoblast differentiation / nucleoside diphosphate kinase activity / dTTP biosynthetic process / response to cadmium ion / cellular response to growth factor stimulus / response to estrogen / mitochondrial matrix / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ostermann, N. / Segura-Pena, D. / Meier, C. / Veit, T. / Monnerjahn, M. / Konrad, M. / Lavie, A. | ||||||
![]() | ![]() Title: Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds Authors: Ostermann, N. / Segura-Pena, D. / Meier, C. / Veit, T. / Monnerjahn, M. / Konrad, M. / Lavie, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 49.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nmxC ![]() 1nmzC ![]() 1nn0C ![]() 1nn1C ![]() 1nn3C ![]() 1nn5C 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23496.900 Da / Num. of mol.: 1 / Mutation: R200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 358 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/FDM.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FDM.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-FDM / | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-ANP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.7 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15-20% PEG 3350, 100 mM Tris/HCl, pH 8.0, 5% filtered dead sea water, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35.8 Å / Num. obs: 34069 / % possible obs: 98.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.264 / % possible all: 98.9 |
Reflection | *PLUS Num. measured all: 169968 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.264 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.6→35.8 Å
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Refinement | *PLUS Num. reflection obs: 34065 / % reflection Rfree: 10 % / Rfactor Rfree: 0.22 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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