- PDB-4bqv: MOUSE CATHEPSIN S WITH COVALENT LIGAND -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4bqv
Title
MOUSE CATHEPSIN S WITH COVALENT LIGAND
Components
CATHEPSIN S
Keywords
HYDROLASE / CYSTEINE PROTEASE
Function / homology
Function and homology information
Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cathepsin S / Degradation of the extracellular matrix / basement membrane disassembly / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / cysteine-type peptidase activity ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cathepsin S / Degradation of the extracellular matrix / basement membrane disassembly / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / cysteine-type peptidase activity / phagocytic vesicle / Neutrophil degranulation / proteolysis involved in protein catabolic process / early endosome lumen / positive regulation of apoptotic signaling pathway / positive regulation of inflammatory response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptidase activity / lysosome / immune response / cysteine-type endopeptidase activity / cell surface / proteolysis / extracellular space / membrane Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 1135 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % Description: 8 INDEPENDENT MOLECULES REFINED IN P1. NO HIGHER SYMMETRY POSSIBLE. ALL 8 ARE SIMILAR, WITH PAIRS AD, BC, EG AND FH BEING ALMOST IDENTICAL. MOLECULES ABCD ARE BETTER DEFINED THAN EFGH.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.7→46 Å / Num. obs: 167038 / % possible obs: 89.2 % / Observed criterion σ(I): -3 / Redundancy: 1.72 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.57
Reflection shell
Resolution: 1.7→1.79 Å / Redundancy: 0.93 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.71 / % possible all: 55
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0029
refinement
XDS
datareduction
SADABS
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN HOUSE STRUCTURES Resolution: 1.7→43.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.807 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BUT NOT OUTPUT. U VALUES REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23997
8262
5 %
RANDOM
Rwork
0.20184
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obs
0.20378
155551
87.49 %
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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