[English] 日本語
![](img/lk-miru.gif)
- PDB-4k5n: Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptida... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4k5n | ||||||
---|---|---|---|---|---|---|---|
Title | Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum | ||||||
![]() | M1 family aminopeptidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / M1 Alanyl-Aminopeptidase / protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | McGowan, S. | ||||||
![]() | ![]() Title: Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum. Authors: Kannan Sivaraman, K. / Paiardini, A. / Sienczyk, M. / Ruggeri, C. / Oellig, C.A. / Dalton, J.P. / Scammells, P.J. / Drag, M. / McGowan, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 387.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 308.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k3nC ![]() 4k5lC ![]() 4k5mC ![]() 4k5oC ![]() 4k5pC ![]() 3ebhS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is the same as asym. |
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 104460.508 Da / Num. of mol.: 1 / Fragment: unp residues 196-1084 / Mutation: N213Q, N223Q, H378P, N501Q, N795Q, N1069QQ Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pTrc-His2b / Production host: ![]() ![]() References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
---|
-Non-polymers , 5 types, 1029 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1OU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1OU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1OU / [( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris, 0.2 M MgCl2, vapor diffusion, hanging drop, temperature 298K, pH 8.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2010 |
Radiation | Monochromator: Double crystal Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95467 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→80.45 Å / Num. all: 1106039 / Num. obs: 77568 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 1.91→2.01 Å / Rmerge(I) obs: 0.63 / % possible all: 98.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: pdb entry 3ebh Resolution: 1.91→80.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.554 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 55.89 Å2 / Biso mean: 21.0848 Å2 / Biso min: 4.07 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→80.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.906→1.956 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 17.676 Å / Origin y: 4.131 Å / Origin z: 10.217 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|