[English] 日本語
![](img/lk-miru.gif)
- PDB-4b12: Plasmodium vivax N-myristoyltransferase with a bound benzofuran i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4b12 | ||||||
---|---|---|---|---|---|---|---|
Title | Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23) | ||||||
![]() | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / PLASMODIUM / MALARIA / DRUG DESIGN | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J. | ||||||
![]() | ![]() Title: Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Anti-Malarial Drug Discovery. Authors: Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 283.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 228.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4b10SC ![]() 4b11C ![]() 4b13C ![]() 4b14C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 45077.594 Da / Num. of mol.: 3 / Fragment: RESIDUES 27-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: SYNTHETIC GENE / Production host: ![]() ![]() References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase |
---|
-Non-polymers , 7 types, 1149 molecules ![](data/chem/img/C23.gif)
![](data/chem/img/NHW.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NHW.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DMS / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | MET26 EQUIVALENT |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.2 M AMMONIUM SULPHATE, 24-26 % PEG 3350, 0.1 M BISTRIS PH 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→55 Å / Num. obs: 118372 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.79→1.84 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4B10 Resolution: 1.79→54.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.11 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.198 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→54.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|