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- PDB-1nn1: Crystal structure of human thymidylate kinase with ddTMP and AppNHp -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nn1 | ||||||
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Title | Crystal structure of human thymidylate kinase with ddTMP and AppNHp | ||||||
![]() | similar to THYMIDYLATE KINASE (DTMP KINASE) | ||||||
![]() | TRANSFERASE / thymidylate kinase / p-loop / dideoxythymidine | ||||||
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 | ![]() | 66.3 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1000.5 KB | Display | ![]() |
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Full document | ![]() | 1006.2 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nmxC ![]() 1nmyC ![]() 1nmzC ![]() 1nn0C ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24052.533 Da / Num. of mol.: 1 / Mutation: R200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-2DT / | #4: Chemical | ChemComp-ANP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.34 % | |||||||||||||||
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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 source | Source: ![]() |
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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: 1.9→71.7 Å / Num. obs: 20663 / % possible obs: 99.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.31 / Rsym value: 0.305 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 127182 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.305 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.9→71.7 Å
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Refinement | *PLUS Num. reflection obs: 20661 / % reflection Rfree: 10 % | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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