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Open data
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Basic information
Entry | Database: PDB / ID: 1npz | ||||||
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Title | Crystal structures of Cathepsin S inhibitor complexes | ||||||
![]() | Cathepsin S | ||||||
![]() | HYDROLASE / Antigen presentation / binding specificity / cysteine proteases / inhibitor complexes / structure-based design / structural plasticity | ||||||
Function / homology | ![]() cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Seddon, A.P. ...Pauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Seddon, A.P. / Menard, R. / Cygler, M. / Rath, V.L. | ||||||
![]() | ![]() Title: Specificity determinants of human cathepsin s revealed by crystal structures of complexes. Authors: Pauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Seddon, A.P. / Menard, R. / Cygler, M. / Rath, V.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1nqcC ![]() 1atkS ![]() 1cj1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24020.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 46.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Sodium Acetate, Ammonium Sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 7, 2001 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 85622 / Num. obs: 83669 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.091 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.503 / % possible all: 96.1 |
Reflection | *PLUS Num. obs: 30379 / Num. measured all: 83669 / Rmerge(I) obs: 0.091 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Search model consists of a polyalanine homology model of cathepsin S constructed from cathepsin K (PDB code 1atk) and Cathepsin L from the procathepsin L (PDB code 1cj1) Resolution: 2→30 Å / σ(F): 0 / σ(I): 0
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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