+Open data
-Basic information
Entry | Database: PDB / ID: 3prs | ||||||
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Title | Endothiapepsin in complex with ritonavir | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Koester, H. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Authors: Behnen, J. / Koster, H. / Neudert, G. / Craan, T. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3prs.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3prs.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 3prs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/3prs ftp://data.pdbj.org/pub/pdb/validation_reports/pr/3prs | HTTPS FTP |
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-Related structure data
Related structure data | 3ms3C 3msaC 3msfC 3msnC 3n21C 3n4aC 3n9wC 3nn7C 3nx8C 3pczC 3pvkC 3pwwC 1oewS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 6 types, 318 molecules
#2: Chemical | ChemComp-RIT / |
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#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-1PE / |
#5: Chemical | ChemComp-PGE / |
#6: Chemical | ChemComp-GOL / |
#7: 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: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M NH4Ac, 0.1M Acetate-Buffer, 26% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: mirrors |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→40 Å / Num. all: 64937 / Num. obs: 64937 / % possible obs: 100 % / Redundancy: 3.7 % / Rsym value: 0.038 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6 / Num. unique all: 2597 / Rsym value: 0.168 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OEW Resolution: 1.38→10 Å / Num. parameters: 25194 / Num. restraintsaints: 31256 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 2248 / Occupancy sum non hydrogen: 2770.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→10 Å
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Refine LS restraints |
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