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Yorodumi- PDB-1hvy: Human thymidylate synthase complexed with dUMP and Raltitrexed, a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hvy | ||||||
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Title | Human thymidylate synthase complexed with dUMP and Raltitrexed, an antifolate drug, is in the closed conformation | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / Tomudex / Raltitrexed | ||||||
Function / homology | Function and homology information uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / G1/S-Specific Transcription / DNA biosynthetic process / developmental growth / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to progesterone / response to cytokine / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Phan, J. / Koli, S. / Minor, W. / Dunlap, R.B. / Berger, S.H. / Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Human thymidylate synthase is in the closed conformation when complexed with dUMP and raltitrexed, an antifolate drug Authors: Phan, J. / Koli, S. / Minor, W. / Dunlap, R.B. / Berger, S.H. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hvy.cif.gz | 249.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hvy.ent.gz | 208.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/1hvy ftp://data.pdbj.org/pub/pdb/validation_reports/hv/1hvy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33111.969 Da / Num. of mol.: 4 / Fragment: RESIDUES 26-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TX61 / References: UniProt: P04818, thymidylate synthase #2: Chemical | ChemComp-D16 / #3: Chemical | ChemComp-UMP / #4: Chemical | ChemComp-BME / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: PEG 4000, EDTA, Tris buffer, Ammonium Sulfate , pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 1998 |
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→6 Å / Num. all: 94011 / Num. obs: 89364 / % possible obs: 95 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→1.96 Å / Rmerge(I) obs: 0.34 / Num. unique all: 8643 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 229821 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1463303.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.58 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / % reflection Rfree: 7.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.288 / % reflection Rfree: 6.4 % / Rfactor Rwork: 0.233 |