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Open data
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Basic information
Entry | Database: PDB / ID: 2yj2 | |||||||||
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Title | CATHEPSIN L WITH A NITRILE INHIBITOR | |||||||||
![]() | CATHEPSIN L1 | |||||||||
![]() | HYDROLASE / DRUG DESIGN / THIOL PROTEASE | |||||||||
Function / homology | ![]() 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 / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / fibronectin binding / Collagen degradation / 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 / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Banner, D.W. / Benz, J.M. / Haap, W. | |||||||||
![]() | ![]() Title: Halogen Bonding at the Active Sites of Human Cathepsin L and Mek1 Kinase: Efficient Interactions in Different Environments. Authors: Hardegger, L.A. / Kuhn, B. / Spinnler, B. / Anselm, L. / Ecabert, R. / Stihle, M. / Gsell, B. / Thoma, R. / Diez, J. / Benz, J.M. / Plancher, J. / Hartmann, G. / Isshiki, Y. / Morikami, K. / ...Authors: Hardegger, L.A. / Kuhn, B. / Spinnler, B. / Anselm, L. / Ecabert, R. / Stihle, M. / Gsell, B. / Thoma, R. / Diez, J. / Benz, J.M. / Plancher, J. / Hartmann, G. / Isshiki, Y. / Morikami, K. / Shimma, N. / Haap, W. / Banner, D.W. / Diederich, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.6 KB | Display | ![]() |
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PDB format | ![]() | 140.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 832.3 KB | Display | ![]() |
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Full document | ![]() | 833.1 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yj8C ![]() 2yj9C ![]() 2yjbC ![]() 2yjcC ![]() 2xu4S 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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Unit cell |
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Components
#1: Protein | Mass: 24191.701 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 114-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-YJ2 / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | CRYSTAL TREATED WITH (2S,4R)-1-[1-(4-BROMO-PHENYL)-CYCLOPROPANE CARBONYL]-4-(2-CHLORO- ...CRYSTAL TREATED WITH (2S,4R)-1-[1-(4-BROMO-PHENYL)-CYCLOPROPA |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.2 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M BIS-TRIS PH 6.5, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→50 Å / Num. obs: 74119 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 6.05 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.12→1.22 Å / Redundancy: 4.82 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.71 / % possible all: 87.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XU4 Resolution: 1.15→45.59 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.686 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS GENERATED IN REFMAC, THOSE WITH ZERO OCCUPANCY REMOVED, U VALUES REFINED INDIVIDUALLY. COVALENT NITRILE BINDING TO CYS25 SG HAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS GENERATED IN REFMAC, THOSE WITH ZERO OCCUPANCY REMOVED, U VALUES REFINED INDIVIDUALLY. COVALENT NITRILE BINDING TO CYS25 SG HAS TARGET BOND LENGTHS C-S 1.75, C-N 1.3 AND PLANAR GEOMETRY.
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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: 17.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→45.59 Å
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Refine LS restraints |
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