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Yorodumi- PDB-5lua: Crystal structure of human legumain (AEP) in complex with compound 11b -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lua | ||||||||||||
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Title | Crystal structure of human legumain (AEP) in complex with compound 11b | ||||||||||||
Components | Legumain | ||||||||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE / ALLOSTERIC INHIBITOR / ASPARAGINYL ENDOPEPTIDASE / ALZHEIMER'S DISEASE | ||||||||||||
Function / homology | Function and homology information negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / vitamin D metabolic process / receptor catabolic process / self proteolysis / endolysosome lumen / activation of cysteine-type endopeptidase activity ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / vitamin D metabolic process / receptor catabolic process / self proteolysis / endolysosome lumen / activation of cysteine-type endopeptidase activity / response to acidic pH / 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Dall, E. / Ye, K. / Brandstetter, H. | ||||||||||||
Citation | Journal: Nat Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lua.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lua.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 5lua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5lua ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lua | HTTPS FTP |
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-Related structure data
Related structure data | 5lu8C 5lu9C 5lubC 4awaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q99538, legumain #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Chemical | ChemComp-5KN / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
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→36.73 Å / Num. obs: 36949 / % possible obs: 95.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AWA Resolution: 2→36.71 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.168 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.189 / 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: 27.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.71 Å
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Refine LS restraints |
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