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- PDB-3oaf: Structural and Kinetic Data for Antifolate Interactions Against P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oaf | ||||||
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Title | Structural and Kinetic Data for Antifolate Interactions Against Pneumocystis jirovecii, Pneumocystis carinii and Human Dihydrofolate Reductase and Thier Active Site Mutants | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE/INHIBITOR / hDHFR inhibitor complexes / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | ![]() regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / 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 / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / glycine biosynthetic 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cody, V. | ||||||
![]() | ![]() Title: Kinetic and structural analysis for potent antifolate inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and human dihydrofolate reductases and their active-site variants. Authors: Cody, V. / Pace, J. / Queener, S.F. / Adair, O.O. / Gangjee, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 39.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 757.6 KB | Display | ![]() |
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Full document | ![]() | 759.1 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l3rC ![]() 4g8zC ![]() 4g95C ![]() 1u72S ![]() 3l3w S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21341.545 Da / Num. of mol.: 1 / Fragment: human dihydrofolate reductase / Mutation: Q35S, N64F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-OAG / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM K2HPO4, 60% saturated Ammonium Sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 21, 2010 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→53.3 Å / Num. all: 31164 / Num. obs: 21273 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.074 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2222 / Rsym value: 0.43 / % possible all: 66.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1u72 Resolution: 1.7→42.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.647 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.905 Å2
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Refine analyze | Luzzati coordinate error obs: 0.217 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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