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Yorodumi- PDB-4x2t: X-ray crystal structure of the orally available aminopeptidase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x2t | |||||||||
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Title | X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M17 Leucyl Aminopeptidase from P. falciparum | |||||||||
Components | M17 leucyl aminopeptidase | |||||||||
Keywords | Hydrolase/Hydrolase Inhibitor / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / TOSEDOSTAT / ANTIMALARIAL / PLASMODIUM FALCIPARUM / Hydrolase-Hydrolase Inhibitor complex | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.729 Å | |||||||||
Authors | Drinkwater, N. / McGowan, S. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Proteins / Year: 2015 Title: X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets PfA-M1 and PfA-M17. Authors: Drinkwater, N. / Bamert, R.S. / Sivaraman, K.K. / Paiardini, A. / McGowan, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x2t.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4x2t.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 4x2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x2t_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 4x2t_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 4x2t_validation.xml.gz | 224.3 KB | Display | |
Data in CIF | 4x2t_validation.cif.gz | 300 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/4x2t ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x2t | HTTPS FTP |
-Related structure data
Related structure data | 4x2uC 3kqxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | biological unit is the same as asym. / biological unit is ta monomer |
-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 57564.648 Da / Num. of mol.: 12 / Fragment: UNP residues 85 to 603 / Mutation: N152Q, N515Q, N545Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: LAP, PF14_0439 / Plasmid: PTRCHIS-2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IL11 |
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-Non-polymers , 6 types, 1101 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-TOD / ( #4: Chemical | ChemComp-CO3 / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-1PE / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 35% (v/v) PEG 400, 0.1 M Tris pH 8.6, 0.2 M Li2SO4 / Temp details: 20 degrees celcius |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.12819 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013 | |||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12819 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.729→48.75 Å / Num. obs: 181046 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.01 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 7.7 / Num. measured all: 664861 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KQX Resolution: 2.729→48.748 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.729→48.748 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 89.2636 Å / Origin y: 56.0604 Å / Origin z: 77.9968 Å
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Refinement TLS group | Selection details: all |