+Open data
-Basic information
Entry | Database: PDB / ID: 3pnr | ||||||
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Title | Structure of PbICP-C in complex with falcipain-2 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Immunoglobulin fold / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Plasmodium berghei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hansen, G. / Hilgenfeld, R. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium. Authors: Hansen, G. / Heitmann, A. / Witt, T. / Li, H. / Jiang, H. / Shen, X. / Heussler, V.T. / Rennenberg, A. / Hilgenfeld, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pnr.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pnr.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/3pnr ftp://data.pdbj.org/pub/pdb/validation_reports/pn/3pnr | HTTPS FTP |
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-Related structure data
Related structure data | 2ghuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27026.479 Da / Num. of mol.: 1 / Fragment: mature FP-2 (UNP residues 245-484) / Mutation: C285A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Escherichia coli (E. coli) / References: UniProt: Q9N6S8 | ||||
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#2: Protein | Mass: 21243.990 Da / Num. of mol.: 1 / Fragment: UNP residues 189-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: PB000502.02.0 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4YW59 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 200 mM sodium acetate, 27.5 mM CdCl2, 100 mM MES, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2009 |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→34.887 Å / Num. obs: 17570 / % possible obs: 95.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GHU Resolution: 2.6→34.887 Å / SU ML: 0.8 / σ(F): 1.73 / 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 / Bsol: 61.714 Å2 / ksol: 0.355 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→34.887 Å
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Refine LS restraints |
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LS refinement shell |
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