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Open data
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Basic information
Entry | Database: PDB / ID: 3pmu | ||||||
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Title | Endothiapepsin in complex with a fragment | ||||||
![]() | Endothiapepsin![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koester, H. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes. Authors: Koster, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.1 KB | Display | ![]() |
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PDB format | ![]() | 56.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3pb5C ![]() 3pbdC ![]() 3pbzC ![]() 3pcwC ![]() 3pgiC ![]() 3pi0C ![]() 3pldC ![]() 3pllC ![]() 3pm4C ![]() 3pmyC ![]() 1oewS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P11838, ![]() |
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#2: Chemical | ChemComp-F7L / ( |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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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 pH 4.6, 26% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 25, 2010 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.43→20 Å / Num. all: 59547 / Num. obs: 59547 / % possible obs: 100 % / Redundancy: 3.1 % / Rsym value: 0.073 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2958 / Rsym value: 0.429 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1OEW Resolution: 1.43→19.698 Å / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.403 Å2 / ksol: 0.441 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.43→19.698 Å
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Refine LS restraints |
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LS refinement shell |
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