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- PDB-5lub: Crystal structure of human legumain (AEP) in complex with compound 11 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lub | ||||||||||||
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Title | Crystal structure of human legumain (AEP) in complex with compound 11 | ||||||||||||
![]() | Legumain | ||||||||||||
![]() | HYDROLASE / CYSTEINE PROTEASE / ALLOSTERIC INHIBITOR / ASPARAGINYL ENDOPEPTIDASE / ALZHEIMER'S DISEASE | ||||||||||||
Function / homology | ![]() negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Dall, E. / Ye, K. / Brandstetter, H. | ||||||||||||
![]() | ![]() Title: Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease. Authors: Zhang, Z. / Obianyo, O. / Dall, E. / Du, Y. / Fu, H. / Liu, X. / Kang, S.S. / Song, M. / Yu, S.P. / Cabrele, C. / Schubert, M. / Li, X. / Wang, J.Z. / Brandstetter, H. / Ye, K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.8 KB | Display | ![]() |
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PDB format | ![]() | 95.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lu8C ![]() 5lu9C ![]() 5luaC ![]() 4awaS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29944.580 Da / Num. of mol.: 2 / Fragment: UNP residues 26-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Chemical | ChemComp-3Y7 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22 % PEG 3350, 0.1 M sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→36.8 Å / Num. obs: 34046 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AWA Resolution: 2.1→36.8 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.818 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.204 / 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: 28.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.8 Å
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Refine LS restraints |
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