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Open data
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Basic information
Entry | Database: PDB / ID: 3pcz | |||||||||
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Title | Endothiapepsin in complex with benzamidine | |||||||||
![]() | Endothiapepsin | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Koester, H. / Heine, A. / Klebe, G. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.4 KB | Display | ![]() |
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PDB format | ![]() | 112.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 440 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ms3C ![]() 3msaC ![]() 3msfC ![]() 3msnC ![]() 3n21C ![]() 3n4aC ![]() 3n9wC ![]() 3nn7C ![]() 3nx8C ![]() 3prsC ![]() 3pvkC ![]() 3pwwC C: citing same article ( |
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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 | #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Ammonium Acetate, 26 % PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.6, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2009 / Details: mirrors |
Radiation | Monochromator: Bertels 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: 1.5→40 Å / Num. all: 51272 / Num. obs: 51272 / % possible obs: 100 % / Redundancy: 3.6 % / Rsym value: 0.08 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2284 / Rsym value: 0.492 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.5→10 Å / Num. parameters: 24077 / Num. restraintsaints: 30348 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 2264 / Occupancy sum non hydrogen: 2651 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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