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Open data
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Basic information
Entry | Database: PDB / ID: 3pm4 | ||||||
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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 | ![]() | 80.8 KB | Display | ![]() |
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PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 682.4 KB | Display | ![]() |
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Full document | ![]() | 682.4 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pb5C ![]() 3pbdC ![]() 3pbzC ![]() 3pcwC ![]() 3pgiC ![]() 3pi0C ![]() 3pldC ![]() 3pllC ![]() 3pmuC ![]() 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, endothiapepsin |
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#2: Chemical | ChemComp-F5N / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % |
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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 277K, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2010 |
Radiation | Monochromator: collimating mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→40 Å / Num. all: 37129 / Num. obs: 37129 / % possible obs: 100 % / Redundancy: 3.9 % / Rsym value: 0.041 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 6 / Num. unique all: 1847 / Rsym value: 0.212 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1OEW Resolution: 1.68→10 Å / Num. parameters: 10867 / Num. restraintsaints: 10117 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 2248.04 / Occupancy sum non hydrogen: 2697.23 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→10 Å
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Refine LS restraints |
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