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- PDB-2hxz: Crystal Structure of Cathepsin S in complex with a Nonpeptidic In... -

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Basic information

Entry
Database: PDB / ID: 2hxz
TitleCrystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor (Hexagonal spacegroup)
ComponentsCathepsin S
KeywordsHYDROLASE / Cathepsin S / Nonpeptidic / chloromethylketone / substrate activity screening
Function / homology
Function and homology information


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 / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / collagen binding / MHC class II antigen presentation / phagocytic vesicle / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling 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
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-H7J / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatterson, A.W. / Wood, W.J. / Hornsby, M. / Lesley, S. / Spraggon, G. / Ellman, J.A.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Identification of selective, nonpeptidic nitrile inhibitors of cathepsin s using the substrate activity screening method.
Authors: Patterson, A.W. / Wood, W.J. / Hornsby, M. / Lesley, S. / Spraggon, G. / Ellman, J.A.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Cathepsin S
B: Cathepsin S
C: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3767
Polymers73,1743
Non-polymers1,2014
Water11,980665
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8563
Polymers24,3911
Non-polymers4652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7602
Polymers24,3911
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7602
Polymers24,3911
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.928, 165.928, 142.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-952-

HOH

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Components

#1: Protein Cathepsin S


Mass: 24391.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-H7J / N-[(1S)-1-{1-[(1R,3E)-1-ACETYLPENT-3-EN-1-YL]-1H-1,2,3-TRIAZOL-4-YL}-1,2-DIMETHYLPROPYL]BENZAMIDE


Mass: 368.473 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.0M Lithium Chloride, 30% PEG 6000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→80 Å / Num. all: 90365 / Num. obs: 90365 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.059 / Net I/σ(I): 23.67
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.12 / Num. unique all: 8924 / Rsym value: 0.747 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H7J

2h7j


Resolution: 1.9→84.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.77 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 6833 5 %RANDOM
Rwork0.21907 ---
obs0.22005 90365 98.9 %-
all-90365 --
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: 23.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.69 Å20 Å2
2--1.39 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 86 665 5861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225374
X-RAY DIFFRACTIONr_bond_other_d0.0010.023641
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9597293
X-RAY DIFFRACTIONr_angle_other_deg1.0753.0068815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09724.228246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83215857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2751523
X-RAY DIFFRACTIONr_chiral_restr0.0730.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021137
X-RAY DIFFRACTIONr_nbd_refined0.1970.21264
X-RAY DIFFRACTIONr_nbd_other0.1870.24189
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22754
X-RAY DIFFRACTIONr_nbtor_other0.0850.22692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2561
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.231
X-RAY DIFFRACTIONr_mcbond_it0.821.54212
X-RAY DIFFRACTIONr_mcbond_other0.1241.51372
X-RAY DIFFRACTIONr_mcangle_it0.93925224
X-RAY DIFFRACTIONr_scbond_it1.58432590
X-RAY DIFFRACTIONr_scangle_it2.2354.52061
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
Num. reflection% reflection
Rwork8633 -
obs-90.07 %

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