[English] 日本語
![](img/lk-miru.gif)
- PDB-1nmz: Crystal structure of human thymidylate kinase with NH2TMP and AppNHp -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1nmz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human thymidylate kinase with NH2TMP and AppNHp | ||||||
![]() | similar to THYMIDYLATE KINASE (DTMP KINASE) | ||||||
![]() | TRANSFERASE / thymidylate kinase / p-loop / aminothymidine | ||||||
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 / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 46.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1nmxC ![]() 1nmyC ![]() 1nn0C ![]() 1nn1C ![]() 1nn3C ![]() 1nn5C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 24052.533 Da / Num. of mol.: 1 / Mutation: R200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-NYM / | #4: Chemical | ChemComp-ANP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.87 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→71.6 Å / Num. obs: 25995 / % possible obs: 97.1 % |
Reflection shell | Resolution: 1.75→1.8 Å / Rsym value: 0.352 / % possible all: 97.2 |
Reflection | *PLUS Num. measured all: 142253 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.352 |
-
Processing
Software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→71.6 Å
| |||||||||||||||
Refinement | *PLUS Num. reflection obs: 25828 / % reflection Rfree: 10 % | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
|