+Open data
-Basic information
Entry | Database: PDB / ID: 8ho4 | |||||||||
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Title | Falcilysin in complex with MMV000848 | |||||||||
Components | Falcilysin | |||||||||
Keywords | HYDROLASE / Falcilysin / MMV000848 / Inhibitor / Complex / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information 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 | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | |||||||||
Authors | Lin, J.Q. / Chung, Z. / Lescar, J. | |||||||||
Funding support | 1items
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Citation | Journal: Cell Chem Biol / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ho4.cif.gz | 277.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ho4.ent.gz | 195.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ho4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ho4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8ho4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8ho4_validation.xml.gz | 44 KB | Display | |
Data in CIF | 8ho4_validation.cif.gz | 67.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8ho4 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8ho4 | HTTPS FTP |
-Related structure data
Related structure data | 7di7C 7diaC 7dijC 8ho5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 135039.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: FLN, PF3D7_1360800 / Production host: Escherichia coli (E. coli) References: UniProt: Q76NL8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases | ||||||
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#2: Chemical | ChemComp-XUH / ( | ||||||
#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05 M Sodium HEPES, 0.05M MOPS pH 7.5, 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen gas / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 92720 / % possible obs: 99.72 % / Redundancy: 13.5 % / Biso Wilson estimate: 29.76 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0615 / Rpim(I) all: 0.01727 / Rrim(I) all: 0.0639 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.501 / Num. unique obs: 8971 / CC1/2: 0.948 / CC star: 0.986 / Rpim(I) all: 0.1464 / Rrim(I) all: 0.5225 / % possible all: 97.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→49.2 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 20.3736 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: 33.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→49.2 Å
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Refine LS restraints |
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LS refinement shell |
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