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Yorodumi- PDB-5hve: 5-methyl-6-(3'-trifluromethoxyphenylthio)[2,3-d]pyrimidine 2,4-diamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hve | ||||||
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Title | 5-methyl-6-(3'-trifluromethoxyphenylthio)[2,3-d]pyrimidine 2,4-diamine | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / dihydrofolate reductase inhibitor complex with NADPH / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Cody, V. | ||||||
Citation | Journal: To Be Published Title: Human dihydrofolate reductase ternary complex with a series of fluorine substituted 5-methyl-6-(4'-methoxyphenythio)[2,3-d]pyrrolo-7-ethyl-2,4-diamines Authors: Cody, V. / Gangjee, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hve.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hve.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hve_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5hve_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5hve_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 5hve_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hve ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hve | HTTPS FTP |
-Related structure data
Related structure data | 5ht4C 5ht5C 1u72S 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
#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 / Plasmid: psd5 / Production host: Escherichia coli (E. coli) / References: UniProt: P00374, dihydrofolate reductase |
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#2: Chemical | ChemComp-65Q / |
#3: Chemical | ChemComp-NDP / |
#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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 100 mM KPO4, ph 6.9, 60% sat AmSO4, 3% ETOH / PH range: 6.7-6.9 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.975 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 14, 2015 / Details: mirrors |
Radiation | Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 35857 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.12 / Rsym value: 0.02 / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.46→1.49 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 4.3 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1u72 Resolution: 1.46→34.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.207 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.047 Å2
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Refinement step | Cycle: 1 / Resolution: 1.46→34.27 Å
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Refine LS restraints |
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