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- PDB-4r5v: Structure of the m1 alanylaminopeptidase from malaria complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r5v | ||||||
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Title | Structure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor | ||||||
![]() | M1 family aminopeptidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / 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 / proteolysis / zinc ion binding / membrane ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Drinkwater, N. / Mcgowan, S. | ||||||
![]() | ![]() Title: Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors. Authors: Mistry, S.N. / Drinkwater, N. / Ruggeri, C. / Sivaraman, K.K. / Loganathan, S. / Fletcher, S. / Drag, M. / Paiardini, A. / Avery, V.M. / Scammells, P.J. / 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 | ![]() | 401.1 KB | Display | ![]() |
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PDB format | ![]() | 322.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4r5tC ![]() 4r5xC ![]() 4r6tC ![]() 4r76C ![]() 4r7mC ![]() 3ebgS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 104460.492 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PTRCHIS-2B / Production host: ![]() ![]() References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-R5V / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % |
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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 pH 8.5, 0.2 M MgCl2, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2014 | ||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.1→46.59 Å / Num. obs: 57652 / % possible obs: 99.5 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.66 Å2 / Rmerge(I) obs: 0.201 / Net I/σ(I): 12.6 | ||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EBG Resolution: 2.1→30.513 Å / SU ML: 0.24 / σ(F): 1.91 / Phase error: 20.78 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.513 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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Refinement TLS params. | Method: refined / Origin x: 17.6033 Å / Origin y: 3.831 Å / Origin z: 10.2029 Å
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Refinement TLS group |
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