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- PDB-4mzs: Mouse cathepsin s with covalent ligand (3S,4S)-1-[(2-CHLOROPHENYL... -

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Basic information

Entry
Database: PDB / ID: 4mzs
TitleMouse cathepsin s with covalent ligand (3S,4S)-1-[(2-CHLOROPHENYL)SULFONYL]-N-[(2E)-2-IMINOETHYL]-4-(MORPHOLIN-4-YLCARBONYL)PYRROLIDINE-3-CARBOXAMIDE
ComponentsCathepsin S
Keywordshydrolase/hydrolase inhibitor / HYDROLASE / CYSTEINE PROTEASE / hydrolase-hydrolase inhibitor complex
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-2EV / Cathepsin S
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKuglstatter, A. / Stihle, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Identification of potent and selective cathepsin S 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. / Sanchez, R.A. / ...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. / Sanchez, R.A. / Iding, H. / Wirz, B. / Haap, W.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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)50,2114
Polymers49,3252
Non-polymers8862
Water4,954275
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1052
Polymers24,6621
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1052
Polymers24,6621
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.542, 88.959, 120.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Gene: Ctss, Cats / Production host: Escherichia coli (E. coli) / References: UniProt: O70370, cathepsin S
#2: Chemical ChemComp-2EV / (3S,4S)-1-[(2-chlorophenyl)sulfonyl]-N-[(2E)-2-iminoethyl]-4-(morpholin-4-ylcarbonyl)pyrrolidine-3-carboxamide


Mass: 442.917 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23ClN4O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.1 M BIS-TRIS, 0.2 M AMMONIUM SULPHATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→44.48 Å / Num. obs: 34621 / % possible obs: 99.9 % / Redundancy: 6.46 % / Biso Wilson estimate: 35.43 Å2 / Rmerge(I) obs: 0.0673 / Net I/σ(I): 13.32
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 6.67 % / Mean I/σ(I) obs: 1.84 / Num. unique all: 4947 / % possible all: 99.8

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BS5

4bs5


Resolution: 1.85→44.48 Å / Cor.coef. Fo:Fc: 0.9305 / Cor.coef. Fo:Fc free: 0.9146 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1743 5.05 %RANDOM
Rwork0.2239 ---
obs0.2264 34521 99.78 %-
Displacement parametersBiso mean: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1-5.6419 Å20 Å20 Å2
2---13.0123 Å20 Å2
3---7.3704 Å2
Refine analyzeLuzzati coordinate error obs: 0.299 Å
Refinement stepCycle: LAST / Resolution: 1.85→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 58 275 3671
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093486HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024718HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1158SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3486HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4292SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.91 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2903 137 4.65 %
Rwork0.2914 2808 -
all0.2914 2945 -
obs--99.78 %

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