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Open data
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Basic information
Entry | Database: PDB / ID: 7agb | ||||||
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Title | Protease Sapp1p from Candida parapsilosis in complex with KB70 | ||||||
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![]() | ANTIBIOTIC / Secreted aspartic protease / virulence factor / candidiasis / peptidomimetic inhibitors | ||||||
Function / homology | ![]() candidapepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dostal, J. / Heidingsfeld, O. / Brynda, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural determinants for subnanomolar inhibition of the secreted aspartic protease Sapp1p from Candida parapsilosis . Authors: Dostal, J. / Brynda, J. / Vankova, L. / Zia, S.R. / Pichova, I. / Heidingsfeld, O. / Lepsik, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 529.2 KB | Display | ![]() |
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PDB format | ![]() | 441.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.5 KB | Display | ![]() |
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Full document | ![]() | 784.6 KB | Display | |
Data in XML | ![]() | 59 KB | Display | |
Data in CIF | ![]() | 84.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7agcC ![]() 7agdC ![]() 7ageC ![]() 3fv3S 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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4 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 8 molecules ABCDIJKL
#1: Protein | Mass: 35865.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein/peptide | Mass: 841.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 6 types, 780 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PE3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PE3.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-PGE / #5: Chemical | #6: Chemical | ChemComp-MES / #7: Chemical | ChemComp-PE3 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100-fold molar inhibitor excess, Cpr=20mg/ml; drops: 0.002ml protein + 0.001ml reservoir; reservoir: 0.1M MES pH 6.5, 30% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 234657 / % possible obs: 98.3 % / Redundancy: 14.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.098 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 15854 / CC1/2: 0.69 / Rrim(I) all: 1.67 / % possible all: 90.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FV3 Resolution: 1.7→34.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.448 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0796 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.08 Å2 / Biso mean: 34.746 Å2 / Biso min: 15.06 Å2
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Refinement step | Cycle: final / Resolution: 1.7→34.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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