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- PDB-4bs6: MOUSE CATHEPSIN S WITH COVALENT LIGAND -

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Basic information

Entry
Database: PDB / ID: 4bs6
TitleMOUSE CATHEPSIN S WITH COVALENT LIGAND
ComponentsCATHEPSIN S
KeywordsHYDROLASE / CYSTEINE PROTEASE / COVALENT LIGAND
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / 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 / cysteine-type peptidase activity / bone resorption ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / 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 / cysteine-type peptidase activity / bone resorption / 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
Chem-JG7 / Cathepsin S
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBanner, D.W. / Benz, J. / Gsell, B. / Stihle, M. / Ruf, A. / Haap, W.
CitationJournal: To be Published
Title: Cathepsin S Nitrile Inhibitors
Authors: Haap, W. / Banner, D.W.
History
DepositionJun 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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
B: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6255
Polymers49,3252
Non-polymers1,3003
Water12,647702
1
A: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3593
Polymers24,6621
Non-polymers6962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2672
Polymers24,6621
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.270, 66.740, 97.960
Angle α, β, γ (deg.)90.00, 90.36, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein CATHEPSIN S


Mass: 24662.480 Da / Num. of mol.: 2 / Fragment: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-JG7 / (2S,4R)-4-[2-chloranyl-4-(4-ethylpiperazin-1-yl)phenyl]sulfonyl-N-[1-(iminomethyl)cyclopropyl]-1-[1-(trifluoromethyl)cyclopropyl]carbonyl-pyrrolidine-2-carboxamide


Mass: 604.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H33ClF3N5O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.8 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG 3350, 0.1 M HEPES PH7.5, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→19.1 Å / Num. obs: 143497 / % possible obs: 82.9 % / Observed criterion σ(I): -3 / Redundancy: 2.74 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.07
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 0.73 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.53 / % possible all: 36.8

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Processing

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

Resolution: 1.2→19.15 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.129 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15497 6353 5.1 %RANDOM
Rwork0.12193 ---
obs0.12359 119007 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.32 Å2
2---0.29 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 86 702 4140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193579
X-RAY DIFFRACTIONr_bond_other_d0.0010.023190
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9724867
X-RAY DIFFRACTIONr_angle_other_deg0.92437386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99924.937158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70115558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5991510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
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_restr1.46836769
X-RAY DIFFRACTIONr_sphericity_free37.3735145
X-RAY DIFFRACTIONr_sphericity_bonded12.09357227
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 318 -
Rwork0.264 5925 -
obs--63.32 %

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