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Open data
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Basic information
Entry | Database: PDB / ID: 7dij | |||||||||
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Title | Falcilysin in complex with MK-4815 | |||||||||
![]() | Falcilysin | |||||||||
![]() | PROTEIN BINDING/INHIBITOR / PROTEIN BINDING-inhibitor complex | |||||||||
Function / homology | ![]() hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / chloroplast / protein processing / metalloendopeptidase activity / mitochondrial matrix / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lin, J.Q. / El Sahili, A. / Lescar, J. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Authors: Wirjanata, G. / Lin, J. / Dziekan, J.M. / El Sahili, A. / Chung, Z. / Tjia, S. / Binte Zulkifli, N.E. / Boentoro, J. / Tham, R. / Jia, L.S. / Go, K.D. / Yu, H. / Partridge, A. / Olsen, D. / ...Authors: Wirjanata, G. / Lin, J. / Dziekan, J.M. / El Sahili, A. / Chung, Z. / Tjia, S. / Binte Zulkifli, N.E. / Boentoro, J. / Tham, R. / Jia, L.S. / Go, K.D. / Yu, H. / Partridge, A. / Olsen, D. / Prabhu, N. / Sobota, R.M. / Nordlund, P. / Lescar, J. / Bozdech, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.3 KB | Display | ![]() |
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PDB format | ![]() | 202.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 75.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7di7C ![]() 7diaC ![]() 8ho4C ![]() 8ho5C ![]() 3s5mS 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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 135039.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q76NL8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 7 types, 1027 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/H8F.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/H8F.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / | ||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-H8F / | #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.48 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.78 Å / Num. obs: 98800 / % possible obs: 99.85 % / Redundancy: 13.2 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1433 / Rpim(I) all: 0.04084 / Rrim(I) all: 0.1491 / Net I/σ(I): 15.48 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.358 / Num. unique obs: 9660 / CC1/2: 0.738 / CC star: 0.922 / Rpim(I) all: 0.3854 / % possible all: 98.83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3S5M Resolution: 1.9→48.78 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2796 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 30.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.78 Å
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Refine LS restraints |
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LS refinement shell |
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