+Open data
-Basic information
Entry | Database: PDB / ID: 4axl | ||||||
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Title | HUMAN CATHEPSIN L APO FORM WITH ZN | ||||||
Components | CATHEPSIN L1 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / fibronectin binding / Collagen degradation / antigen processing and presentation / collagen catabolic process / serpin family protein binding / Attachment and Entry / cysteine-type peptidase activity / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / lysosome / symbiont entry into host cell / immune response / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Banner, D.W. / Benz, J. | ||||||
Citation | Journal: Chemmedchem / Year: 2013 Title: Optimization of Triazine Nitriles as Rhodesain Inhibitors: Structure-Activity Relationships, Bioisosteric Imidazopyridine Nitriles, and X-Ray Crystal Structure Analysis with Human Cathepsin L Authors: Ehmke, V. / Winkler, E. / Banner, D.W. / Haap, W. / Schweizer, W.B. / Rottmann, M. / Kaiser, M. / Freymond, C. / Schirmeister, T. / Diederich, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4axl.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4axl.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 4axl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4axl ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4axl | HTTPS FTP |
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-Related structure data
Related structure data | 4axmC 2yjcS 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
#1: Protein | Mass: 24191.701 Da / Num. of mol.: 1 / Fragment: CATALYTIC, RESIDUES 114-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07711, cathepsin L |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→48.15 Å / Num. obs: 24483 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 17.88 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.92→2.02 Å / Redundancy: 18.34 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.41 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YJC Resolution: 1.92→46.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.501 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS COMPUTED BY REFMAC AT RIDING POSITIONS NOT OUTPUT. THE ZN ION BRIDGES THE ACTIVE SITE CYS AND HIS RESIDUES TO A GLU FROM ANOTHER MOLECULE TO FORM A DIMER. AN UNIDENTIFIED BUFFER ...Details: HYDROGENS COMPUTED BY REFMAC AT RIDING POSITIONS NOT OUTPUT. THE ZN ION BRIDGES THE ACTIVE SITE CYS AND HIS RESIDUES TO A GLU FROM ANOTHER MOLECULE TO FORM A DIMER. AN UNIDENTIFIED BUFFER MOLECULE BINDING ACROSS A DIAD AXIS IS MARKED BY AN ACETATE MOLECULE
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.997 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→46.67 Å
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