+Open data
-Basic information
Entry | Database: PDB / ID: 1e2q | ||||||
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Title | Human thymidylate kinase complexed with TP5A and a magnesium-ion | ||||||
Components | THYMIDYLATE KINASE | ||||||
Keywords | 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: 1.7 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 | 1e2q.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e2q.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e2q_validation.pdf.gz | 521.1 KB | Display | wwPDB validaton report |
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Full document | 1e2q_full_validation.pdf.gz | 526.6 KB | Display | |
Data in XML | 1e2q_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1e2q_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2q ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2q | HTTPS FTP |
-Related 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-ATP / | ||||||
#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: 2.62 Å3/Da / Density % sol: 53.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.3 Å / Num. obs: 27940 / % possible obs: 97.4 % / Redundancy: 5.3 % / Rsym value: 0.033 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.222 / % possible all: 89.3 |
Reflection | *PLUS Num. measured all: 148714 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 89.3 % / Rmerge(I) obs: 0.222 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: TP5A IS A BISUBSTRATE INHIBITOR THAT CAN BE THOUGHT OF A CONSISTING OF ATP AND TMP JOINED BY A LINKER PHOSPHATE. THE LATTER IS NOT VISIBLE IN THE ELECTRON DENSITY MAP. THEREFORE, WE MODELED ...Details: TP5A IS A BISUBSTRATE INHIBITOR THAT CAN BE THOUGHT OF A CONSISTING OF ATP AND TMP JOINED BY A LINKER PHOSPHATE. THE LATTER IS NOT VISIBLE IN THE ELECTRON DENSITY MAP. THEREFORE, WE MODELED THE NUCLEOTIDE AS ATP AND TMP.
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Refinement step | Cycle: LAST / Resolution: 1.7→35.3 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.192 / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |