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- PDB-6qcb: Crystal structure of human cathepsin D in complex with macrocycli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qcb | ||||||||||||
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Title | Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 9 | ||||||||||||
![]() | (Cathepsin D) x 2 | ||||||||||||
![]() | HYDROLASE / aspartic protease / peptidomimetic inhibitor | ||||||||||||
Function / homology | ![]() cathepsin D / aspartic-type peptidase activity / regulation of establishment of protein localization / insulin catabolic process / lipoprotein catabolic process / insulin receptor recycling / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Collagen degradation / autophagosome assembly / Metabolism of Angiotensinogen to Angiotensins ...cathepsin D / aspartic-type peptidase activity / regulation of establishment of protein localization / insulin catabolic process / lipoprotein catabolic process / insulin receptor recycling / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Collagen degradation / autophagosome assembly / Metabolism of Angiotensinogen to Angiotensins / Insulin receptor recycling / MHC class II antigen presentation / lysosomal lumen / endosome lumen / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / melanosome / tertiary granule lumen / peptidase activity / collagen-containing extracellular matrix / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / aspartic-type endopeptidase activity / lysosome / endosome membrane / positive regulation of apoptotic process / membrane raft / lysosomal membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Brynda, J. / Houstecka, R. / Majer, P. / Mares, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis. Authors: Houstecka, R. / Hadzima, M. / Fanfrlik, J. / Brynda, J. / Pallova, L. / Hanova, I. / Mertlikova-Kaiserova, H. / Lepsik, M. / Horn, M. / Smrcina, M. / Majer, P. / Mares, 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 | ![]() | 95.8 KB | Display | ![]() |
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PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qbgC ![]() 6qbhSC 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 10688.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 26370.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 327 molecules ![](data/chem/img/PO3.gif)
![](data/chem/img/HWE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HWE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PO3 / | ||
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#6: Chemical | ChemComp-HWE / ( | ||
#7: Chemical | ChemComp-DMS / | ||
#8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 25 % PEG 3350 0.2 lithium sulphate 0.1 Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 62404 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.55→1.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.02 / CC1/2: 0.622 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QBH Resolution: 1.55→43.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.452 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.435 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→43.75 Å
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Refine LS restraints |
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