[English] 日本語
![](img/lk-miru.gif)
- PDB-4osg: Klebsiella pneumoniae complexed with NADPH and 6-ethyl-5-[(3R)-3-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4osg | ||||||
---|---|---|---|---|---|---|---|
Title | Klebsiella pneumoniae complexed with NADPH and 6-ethyl-5-[(3R)-3-[3-methoxyl-5-(pyridine-4-yl)phenyl]but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP1006) | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | Oxidoreductase/Oxidoreductase inhibitor / Oxidoreductase / hydride shift / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | ![]() Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lamb, K.M. / Anderson, A.C. | ||||||
![]() | ![]() Title: Crystal Structures of Klebsiella pneumoniae Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal Features for Potency and Selectivity. Authors: Lamb, K.M. / Lombardo, M.N. / Alverson, J. / Priestley, N.D. / Wright, D.L. / Anderson, A.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 145.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 116.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 18813.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 8 types, 31 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/06U.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/06U.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-06U / #4: Chemical | ChemComp-EOH / | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PEG / | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.02 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100 mM cacodylate pH7.4, 125 mM sodium acetate, 25% (w/v) PEG 8000, 11 mM calcium chloride, 11 mM bentaine hydrochloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2013 |
Radiation | Monochromator: A KOHZU double crystal monochromator with a sagittally focused second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→39.27 Å / Num. all: 20988 / Num. obs: 19813 / % possible obs: 94.4 % / Observed criterion σ(F): 13.4 / Observed criterion σ(I): 13.4 / Redundancy: 1.67 % / Rmerge(I) obs: 0.049 / Rsym value: 0.07 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.468 / % possible all: 95.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→39.27 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|