[English] 日本語
Yorodumi- PDB-3k47: Alternate Binding Modes Observed for the E- and Z-Isomers of 2,4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k47 | ||||||
---|---|---|---|---|---|---|---|
Title | Alternate Binding Modes Observed for the E- and Z-Isomers of 2,4-Diaminofuro[2,3-d]pyrimidines as Ternary Complexes with NADPH and Mouse Dihydrofolate Reductase | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / MOUSE DIHYDROFOLATE REDUCTASE COFACTOR LIGAND COMPLEX / NADP / ONE-CARBON METABOLISM | ||||||
Function / homology | Function and homology information Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / tetrahydrofolate interconversion / axon regeneration ...Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / tetrahydrofolate interconversion / axon regeneration / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / response to nicotine / positive regulation of nitric-oxide synthase activity / NADP binding / mitochondrial inner membrane / mitochondrial matrix / mRNA binding / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Cody, V. / Pace, J. / Queener, S.F. / Gangjee, A. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2009 Title: Design, synthesis, and X-ray crystal structures of 2,4-diaminofuro[2,3-d]pyrimidines as multireceptor tyrosine kinase and dihydrofolate reductase inhibitors. Authors: Gangjee, A. / Li, W. / Lin, L. / Zeng, Y. / Ihnat, M. / Warnke, L.A. / Green, D.W. / Cody, V. / Pace, J. / Queener, S.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3k47.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3k47.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k47 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k47 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3k45C 2fzjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21503.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhfr / Plasmid: PPH70D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: P00375, dihydrofolate reductase |
---|---|
#2: Chemical | ChemComp-D09 / |
#3: Chemical | ChemComp-NDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % |
---|---|
Crystal grow | pH: 8.3 Details: 200 MM TRIS, PH 8.3, 85 MM NA CACODYLATE, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 24, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→23.85 Å / Num. obs: 10815 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.079 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.32 / % possible all: 92.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FZJ Resolution: 2.05→21.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.48 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→21.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
|