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Open data
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Basic information
Entry | Database: PDB / ID: 3pvk | |||||||||
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Title | Secreted aspartic protease 2 in complex with benzamidine | |||||||||
![]() | Candidapepsin-2 | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() : / protein catabolic process => GO:0030163 / candidapepsin / : / signal peptide processing / fungal-type cell wall organization / adhesion of symbiont to host / : / fungal-type cell wall / protein metabolic process ...: / protein catabolic process => GO:0030163 / candidapepsin / : / signal peptide processing / fungal-type cell wall organization / adhesion of symbiont to host / : / fungal-type cell wall / protein metabolic process / protein catabolic process / extracellular vesicle / aspartic-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
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 | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ms3C ![]() 3msaC ![]() 3msfC ![]() 3msnC ![]() 3n21C ![]() 3n4aC ![]() 3n9wC ![]() 3nn7C ![]() 3nx8C ![]() 3pczC ![]() 3prsC ![]() 3pwwC ![]() 1eagS S: Starting model for refinement 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36357.723 Da / Num. of mol.: 1 / Fragment: UNP residues 57-398 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P28871, UniProt: P0CS83*PLUS, candidapepsin |
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-Non-polymers , 5 types, 338 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 9 mM ZnAc, 16% PEG 8000, 0.1M imidazole/malate buffer pH 6.5, VAPOR DIFFUSION, SITTING DROP, 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: Jul 31, 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: 1.27→40 Å / Num. all: 79920 / Num. obs: 79920 / % possible obs: 100 % / Redundancy: 6.8 % / Rsym value: 0.071 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3341 / Rsym value: 0.418 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EAG Resolution: 1.27→38.999 Å / SU ML: 0.12 / σ(F): 0 / 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: 39.22 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.27→38.999 Å
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Refine LS restraints |
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LS refinement shell |
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