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- PDB-3h8b: A combined crystallographic and molecular dynamics study of cathe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h8b | ||||||
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Title | A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors(compound 9) | ||||||
![]() | Cathepsin L1 | ||||||
![]() | HYDROLASE / cysteine proteases / Cathepsin L / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tulsidas, S.R. / Chowdhury, S.F. / Kumar, S. / Joseph, L. / Purisima, E.O. / Sivaraman, J. | ||||||
![]() | ![]() Title: A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors Authors: Shenoy, R.T. / Chowdhury, S.F. / Kumar, S. / Joseph, L. / Purisima, E.O. / Sivaraman, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268.1 KB | Display | ![]() |
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PDB format | ![]() | 228.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 68.4 KB | Display | |
Data in CIF | ![]() | 84.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24191.701 Da / Num. of mol.: 6 Fragment: Cathepsin L Heavy Chain and Light Chain, UNP residues 114-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NSY / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 116974 / Rsym value: 0.06 / Net I/σ(I): 17.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 40.919 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 101.66 Å2 / Biso mean: 27.671 Å2 / Biso min: 8.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45 Å
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Refine LS restraints |
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