- PDB-7fqi: Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-... -
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Entry
Database: PDB / ID: 7fqi
Title
Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide
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 / negative regulation of gene expression / cysteine-type endopeptidase activity / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 23.4mg/mL deglycosylated protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 25% v/v ...Details: 23.4mg/mL deglycosylated protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 25% v/v PEG smear broad, 0.1M Bicine/NaOH pH 9.0, 10% v/v 2-Propanol, total volume 200nL
Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 1.45→70.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.36 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Ligand in chain B has alternate conformations for the difluorophenyl
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1891
7076
5 %
RANDOM
Rwork
0.1668
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obs
0.1679
134406
67 %
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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: MASK
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