+Open data
-Basic information
Entry | Database: PDB / ID: 1nn0 | ||||||
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Title | Crystal structure of human thymidylate kinase with ddTMP and ADP | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE / thymidylate kinase / p-loop / dideoxythymidine | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Ostermann, N. / Segura-Pena, D. / Meier, C. / Veit, T. / Monnerjahn, M. / Konrad, M. / Lavie, A. | ||||||
Citation | Journal: Biochemistry / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nn0.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nn0.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nn0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1nn0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1nn0_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1nn0_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/1nn0 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/1nn0 | HTTPS FTP |
-Related structure data
Related structure data | 1nmxC 1nmyC 1nmzC 1nn1C 1nn3C 1nn5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Homo sapiens (human) / Gene: DTYMK OR TYMK OR TMPK OR CDC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P23919, dTMP kinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-2DT / | #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.12 % | |||||||||||||||
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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: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9887 Å |
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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: 0.9887 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→70.7 Å / Num. obs: 35723 / % possible obs: 96.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.24 |
Reflection shell | Resolution: 1.55→1.6 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.32 / Rsym value: 0.364 / % possible all: 96.4 |
Reflection | *PLUS % possible obs: 94.7 % / Num. measured all: 119378 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→50.3 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.6→50.3 Å
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Refinement | *PLUS Lowest resolution: 70.7 Å / Num. reflection obs: 32480 / % reflection Rfree: 10 % | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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