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Yorodumi- PDB-1s3v: Structure Determination of Tetrahydroquinazoline Antifolates in C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s3v | ||||||
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Title | Structure Determination of Tetrahydroquinazoline Antifolates in Complex with Human and Pneumocystis carinii Dihydrofolate Reductase: Correlations of Enzyme Selectivity and Stereochemistry | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / dihydrofolate reductase / inhibitor / stereochemistry | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Cody, V. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Queener, S.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure determination of tetrahydroquinazoline antifolates in complex with human and Pneumocystis carinii dihydrofolate reductase: correlations between enzyme selectivity and stereochemistry. Authors: Cody, V. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Queener, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s3v.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s3v.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 1s3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/1s3v ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s3v | HTTPS FTP |
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-Related 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: 21349.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Production host: Escherichia coli (E. coli) / References: UniProt: P00374, dihydrofolate reductase | ||||
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#2: Chemical | #3: Chemical | ChemComp-TQD / ( | #4: 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: 45.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 60-65% ammonium sulfate, 0.1 M phosphate buffer, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K | ||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418,1.5621,1.7321 | ||||||||||||
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 20, 1998 / Details: mirrors | ||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. all: 15660 / Num. obs: 13649 / % possible obs: 90.3 % / Observed criterion σ(F): 0.016 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.042 | ||||||||||||
Reflection shell | Resolution: 1.8→1.81 Å / % possible all: 55.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.5 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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