+Open data
-Basic information
Entry | Database: PDB / ID: 4awb | ||||||
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Title | Crystal structure of active legumain in complex with AAN-CMK | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE / CYSTEINE PROTEASE / LYSOSOMAL / AEP / SUBSTRATE SPECIFICITY / MHCII / ANTIGEN PROCESSING / CANCER | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Dall, E. / Brandstetter, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Mechanistic and Structural Studies on Legumain Explain its Zymogenicity, Distinct Activation Pathways, and Regulation Authors: Dall, E. / Brandstetter, H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4awb.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4awb.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 4awb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4awb_validation.pdf.gz | 486.2 KB | Display | wwPDB validaton report |
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Full document | 4awb_full_validation.pdf.gz | 492.8 KB | Display | |
Data in XML | 4awb_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 4awb_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/4awb ftp://data.pdbj.org/pub/pdb/validation_reports/aw/4awb | HTTPS FTP |
-Related structure data
Related structure data | 4aw9SC 4awaC 4fguC 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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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 10 molecules ABIJ
#1: Protein | Mass: 32273.203 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-309 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: LEISHMANIA TARENTOLAE (eukaryote) / Strain (production host): P10 / References: UniProt: Q99538, legumain #2: Protein/peptide | #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 97 molecules
#4: Chemical | #5: Chemical | ChemComp-HG / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 2.26 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.2 M LITHIUMSULFATE MONOHYDRATE, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0032 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0032 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.56→72.19 Å / Num. obs: 17704 / % possible obs: 95.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.8 | |||||||||||||||
Reflection shell | Resolution: 2.56→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AW9 Resolution: 2.7→63.91 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.853 / SU B: 15.682 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.891 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→63.91 Å
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Refine LS restraints |
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