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Yorodumi- PDB-1e2d: Human thymidylate kinase complexed with thymidine monophosphate, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e2d | ||||||
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Title | Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion | ||||||
Components | THYMIDYLATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / THYMIDYLATE KINASE / P-LOOP | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ostermann, N. / Schlichting, I. / Brundiers, R. / Konrad, M. / Reinstein, J. / Veit, T. / Goody, R.S. / Lavie, A. | ||||||
Citation | Journal: Structure / Year: 2000 Title: Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained from Crystal Structures of Enzyme Complexes Along the Reaction Coordinate Authors: Ostermann, N. / Schlichting, I. / Brundiers, R. / Konrad, M. / Reinstein, J. / Veit, T. / Goody, R.S. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e2d.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e2d.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e2d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1e2d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1e2d_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1e2d_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2d ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2d | HTTPS FTP |
-Related structure data
Related structure data | 1e2eC 1e2fC 1e2gC 1e2qC 3tmkS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24052.533 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23919, dTMP kinase | ||||||
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#2: Chemical | ChemComp-TMP / | ||||||
#3: Chemical | ChemComp-ADP / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CHAIN A ENGINEERED | Sequence details | SAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON ...SAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON DENSITY OF SIDE-CHAINS). POSSIBLE ERROR IN SWISSPROT ENTRY. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: VAPOR DIFFUSION AT 293 K MIXING 2 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% PEG 3350, 100 MM TRIS HCL PH 8. ...Details: VAPOR DIFFUSION AT 293 K MIXING 2 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% PEG 3350, 100 MM TRIS HCL PH 8.0 AND 50 MICROLITERS OF DEAD SEA WATER. AN ADP,TMP COCRYSTAL WAS SOAKED OVERNIGHT IN 250 MM NAF AND 80 MM ALCL3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Aug 15, 1998 |
Radiation | Monochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→33.46 Å / Num. obs: 31064 / % possible obs: 95.7 % / Redundancy: 10.5 % / Rsym value: 0.061 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.63→1.7 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4 / Rsym value: 0.203 / % possible all: 75.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TMK Resolution: 1.65→33.4 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: GLU 152 MODELED AS ALA AND LYS 205 MODELED AS ALA DUE TO WEAK SIDE-CHAIN ELECTRON DENSITY
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Refinement step | Cycle: LAST / Resolution: 1.65→33.4 Å
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Refine LS restraints |
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