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Yorodumi- PDB-1ju6: Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ju6 | ||||||
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Title | Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrrolo(2,3-d)pyrimidine-based Antifolate | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / antifolate / dTMP synthesis / drug resistance / cancer | ||||||
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 / thymidylate synthase / response to vitamin A / 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 / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / 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: 2.89 Å | ||||||
Authors | Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases. Authors: Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M. #1: Journal: Biochemistry / Year: 1995 Title: Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site Authors: Schiffer, C.A. / Clifton, I.J. / Davisson, V.J. / Santi, D.V. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ju6.cif.gz | 238.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ju6.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ju6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1ju6 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1ju6 | HTTPS FTP |
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-Related structure data
-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: 35734.859 Da / Num. of mol.: 4 / Mutation: R46E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGCHTS-TAA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P04818, thymidylate synthase #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-UMP / #4: Chemical | ChemComp-LYA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG-monomethyl ether 5000, sodium cacodylate, ammonium sulfate, KCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å | ||||||||||||||||||
Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.8→23 Å / Num. all: 24659 / Num. obs: 24659 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.4 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.88 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: thymidylate synthase portion of the Leishmania major DHFR-TS bifunctional enzyme Resolution: 2.89→22.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 173248.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues 1 through 27 in each chain are disordered and were not included in refinement. All four monomers in the asymmetric unit were initially constrained to have equivalent structures. NCS ...Details: Residues 1 through 27 in each chain are disordered and were not included in refinement. All four monomers in the asymmetric unit were initially constrained to have equivalent structures. NCS constraints were relaxed to restraints in the final cycles of refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.305 Å2 / ksol: 0.361834 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.89→22.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.89→3.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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