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- PDB-4zw8: X-ray crystal structure of PfA-M1 in complex with hydroxamic acid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zw8 | ||||||
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Title | X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 9r | ||||||
![]() | M1 family aminopeptidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / M1 ALANYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / 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. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions. Authors: Drinkwater, N. / Vinh, N.B. / Mistry, S.N. / Bamert, R.S. / Ruggeri, C. / Holleran, J.P. / Loganathan, S. / Paiardini, A. / Charman, S.A. / Powell, A.K. / Avery, V.M. / McGowan, S. / Scammells, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 420.2 KB | Display | ![]() |
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PDB format | ![]() | 337.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zw3C ![]() 4zw5C ![]() 4zw6C ![]() 4zw7C ![]() 4zx3C ![]() 4zx4C ![]() 4zx5C ![]() 4zx6C ![]() 4zx8C ![]() 4zx9C ![]() 4zy0C ![]() 4zy1C ![]() 4zy2C ![]() 4zyqC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 103760.719 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084 / Mutation: N213Q, N223Q, H378P, N501Q, N795Q, N1069Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / Production host: ![]() ![]() References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Non-polymers , 5 types, 938 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/4T2.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4T2.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-4T2 / | ||||
#4: Chemical | ChemComp-DMS / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 14, 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→35.69 Å / Num. obs: 66805 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.065 / Net I/σ(I): 8.5 / Num. measured all: 447176 / Scaling rejects: 41 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EBG Resolution: 2→35.688 Å / FOM work R set: 0.8604 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.97 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.73 Å2 / Biso mean: 27.11 Å2 / Biso min: 7.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→35.688 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: 24
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Refinement TLS params. | Method: refined / Origin x: 93.2173 Å / Origin y: 113.0877 Å / Origin z: 128.5903 Å
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Refinement TLS group |
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