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- PDB-4bsq: MOUSE CATHEPSIN S WITH COVALENT LIGAND -

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Basic information

Entry
Database: PDB / ID: 4bsq
TitleMOUSE CATHEPSIN S WITH COVALENT LIGAND
ComponentsCATHEPSIN S
KeywordsHYDROLASE / CYSTEINE PROTEASE
Function / homology
Function and homology information


Assembly of collagen fibrils and other multimeric structures / Trafficking and processing of endosomal TLR / cathepsin S / basement membrane disassembly / Degradation of the extracellular matrix / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / phagocytic vesicle ...Assembly of collagen fibrils and other multimeric structures / Trafficking and processing of endosomal TLR / cathepsin S / basement membrane disassembly / Degradation of the extracellular matrix / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / phagocytic vesicle / cysteine-type peptidase activity / Neutrophil degranulation / early endosome lumen / proteolysis involved in protein catabolic process / 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
Chem-QQV / Cathepsin S
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBanner, D.W. / Benz, J. / Gsell, B. / Stihle, M. / Ruf, A. / Hilpert, H.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Identification of Potent and Selective Cathepsin S (Cats) Inhibitors Containing Different Central Cyclic Scaffolds.
Authors: Hilpert, H. / Mauser, H. / Humm, R. / Anselm, L. / Kuehne, H. / Hartmann, G. / Gruener, S. / Banner, D.W. / Benz, J. / Gsell, B. / Kuglstatter, A. / Stihle, M. / Thoma, R. / Alvarez-Sanchez, ...Authors: Hilpert, H. / Mauser, H. / Humm, R. / Anselm, L. / Kuehne, H. / Hartmann, G. / Gruener, S. / Banner, D.W. / Benz, J. / Gsell, B. / Kuglstatter, A. / Stihle, M. / Thoma, R. / Alvarez-Sanchez, R. / Iding, H. / Wirz, B. / Haap, W.
History
DepositionJun 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4546
Polymers24,6621
Non-polymers7925
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.340, 66.790, 53.730
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2141-

HOH

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Components

#1: Protein CATHEPSIN S


Mass: 24662.480 Da / Num. of mol.: 1 / Fragment: CATHEPSIN S, RESIDUES 116-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O70370, cathepsin S
#2: Chemical ChemComp-QQV / (1R,2R,4R)-N-(2-azanylideneethyl)-2-morpholin-4-ylcarbonyl-4-(phenylsulfonyl)cyclopentane-1-carboxamide


Mass: 407.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N3O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Sequence details116-340 NO MUTATIONS 218 MET IS VARIANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.5 % / Description: NONE
Crystal growpH: 5.5 / Details: 2M AM2SO4, 0.1M BISTRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→49.45 Å / Num. obs: 16810 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.83
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.28 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE STRUCTURES

Resolution: 1.96→18.66 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.921 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21233 850 5.1 %RANDOM
Rwork0.17417 ---
obs0.17616 15958 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.05 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.96→18.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 48 161 1885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191772
X-RAY DIFFRACTIONr_bond_other_d0.0010.021551
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9692402
X-RAY DIFFRACTIONr_angle_other_deg0.7313.0043576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73424.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87215274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.708155
X-RAY DIFFRACTIONr_chiral_restr0.0750.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.963→2.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 55 -
Rwork0.266 1036 -
obs--83.92 %

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