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- PDB-8cqa: Mycobacterium tuberculosis dihydrofolate reductase in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cqa | ||||||
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Title | Mycobacterium tuberculosis dihydrofolate reductase in complex with N-(4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)phenyl)acetamide | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Dihydrofolate reductase Mycobacterium tuberculosis | ||||||
Function / homology | : / Chem-NDP / : / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kirkman, T.J. / Dias, M.V.B. / Coyne, A.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Expansion of a series of pyrimidine derivatives utilising fragment-based merging leads to increased affinity to Mycobacterium tuberculosis dihydrofolate reductase (unpublished currently) Authors: Kirkman, T.J. / Dias, M.V.B. / Coyne, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.1 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cq8C ![]() 8cq9C C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17660.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 64 molecules ![](data/chem/img/NDP.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | Mass: 311.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N5O / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-MES / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M ammonium sulphate, 100 mM MES, 10 mM CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.76 Å / Num. obs: 22315 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Net I/σ(I): 14.9 / Num. measured all: 283162 |
Reflection shell | Resolution: 2→2.11 Å / % possible obs: 100 % / Redundancy: 12.7 % / Num. measured all: 40858 / Num. unique obs: 3215 / CC1/2: 0.834 / Rpim(I) all: 0.342 / Rrim(I) all: 1.234 / Net I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.76 Å
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Refine LS restraints |
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LS refinement shell |
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