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- PDB-4k5o: Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptida... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k5o | ||||||
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Title | Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum | ||||||
![]() | M1 family aminopeptidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / M1 Alanyl-Aminopeptidase / ![]() | ||||||
Function / homology | ![]() symbiont-containing vacuole membrane / vacuolar lumen / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410 KB | Display | ![]() |
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PDB format | ![]() | 329.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4k3nC ![]() 4k5lC ![]() 4k5mC ![]() 4k5nC ![]() 4k5pC ![]() 3ebhS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
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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, ![]() |
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-Non-polymers , 5 types, 1020 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/1OT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/1OT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-1OT / {( | #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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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 |
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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![]() |
Reflection | Resolution: 1.9→80.37 Å / Num. all: 1113693 / Num. obs: 75260 / % possible obs: 96.4 % / Rmerge(I) obs: 0.144 |
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Processing
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Refinement | Starting model: 3EBH Resolution: 1.9→64.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.082 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 57.91 Å2 / Biso mean: 20.831 Å2 / Biso min: 4.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→64.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.903→1.953 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.676 Å / Origin y: 4.131 Å / Origin z: 10.217 Å
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Refinement TLS group |
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