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- PDB-1pdb: Analysis of Three Crystal Structure Determinations of a 5-Methyl-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pdb | ||||||
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Title | Analysis of Three Crystal Structure Determinations of a 5-Methyl-6-N-Methylanilino Pyridopyrimidine Antifolate Complex with Human Dihydrofolate Reductase | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / human dihydrofolate reductase inhibitor complexes | ||||||
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. / Luft, J.R. / Pangborn, W. / Gangjee, A. | ||||||
![]() | ![]() Title: Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase. Authors: Cody, V. / Luft, J.R. / Pangborn, W. / 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 | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.5 KB | Display | ![]() |
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Full document | ![]() | 459.1 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pd8C ![]() 1pd9C ![]() 1hfpS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, 0.1 M phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 3, 1994 / Details: mirrors |
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: 2.1→8 Å / Num. all: 9522 / Num. obs: 8535 / % possible obs: 80.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 51.9 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 51.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HFP Resolution: 2.2→8 Å / Isotropic thermal model: isotropic / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.7 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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