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- PDB-2op3: The structure of cathepsin S with a novel 2-arylphenoxyacetaldehy... -

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Basic information

Entry
Database: PDB / ID: 2op3
TitleThe structure of cathepsin S with a novel 2-arylphenoxyacetaldehyde inhibitor derived by the Substrate Activity Screening (SAS) method
ComponentsCathepsin S
KeywordsHYDROLASE / Cathepsin S / NONpeptidic / Substrate Activity Screening
Function / homology
Function and homology information


cathepsin S / regulation of antigen processing and presentation / 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 ...cathepsin S / regulation of antigen processing and presentation / 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 / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / collagen binding / laminin binding / phagocytic vesicle / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / protein processing / tertiary granule lumen / late endosome / : / ficolin-1-rich granule lumen / adaptive immune response / lysosome / immune response / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / 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
2-[(2',3',4'-TRIFLUOROBIPHENYL-2-YL)OXY]ETHANOL / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSpraggon, G. / Inagaki, H. / Tsuruoka, H. / Hornsby, M. / Lesley, S.A. / Ellman, J.A.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Characterization and optimization of selective, nonpeptidic inhibitors of cathepsin S with an unprecedented binding mode.
Authors: Inagaki, H. / Tsuruoka, H. / Hornsby, M. / Lesley, S.A. / Spraggon, G. / Ellman, J.A.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: 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 / pdbx_struct_special_symmetry / 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
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,6376
Polymers48,7832
Non-polymers1,8544
Water8,557475
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9774
Polymers24,3911
Non-polymers1,5863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6602
Polymers24,3911
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Cathepsin S
B: Cathepsin S
hetero molecules

A: Cathepsin S
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,27412
Polymers97,5664
Non-polymers3,7088
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area7470 Å2
ΔGint-54 kcal/mol
Surface area34650 Å2
MethodPISA
4
A: Cathepsin S
hetero molecules

A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9548
Polymers48,7832
Non-polymers3,1726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area2580 Å2
ΔGint-45 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.384, 85.384, 151.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-701-

SO4

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Components

#1: Protein Cathepsin S


Mass: 24391.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CATHS / 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-TF5 / 2-[(2',3',4'-TRIFLUOROBIPHENYL-2-YL)OXY]ETHANOL


Mass: 268.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11F3O2
#4: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaAcetate, 20% Peg-8000 and 2.0M Li2SO4, 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 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→43.4 Å / Num. all: 74679 / Num. obs: 74679 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 45.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 5 / Num. unique all: 7367 / Rsym value: 0.725 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2F1G

2f1g


Resolution: 1.6→43.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.098 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18063 3738 5 %RANDOM
Rwork0.15815 ---
all0.15929 ---
obs0.15929 70645 100 %-
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: 13.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 63 475 3955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223580
X-RAY DIFFRACTIONr_bond_other_d0.0020.022430
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9574846
X-RAY DIFFRACTIONr_angle_other_deg0.8333.0035895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14624.371167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.52815570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2931515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_nbd_refined0.2110.2756
X-RAY DIFFRACTIONr_nbd_other0.1950.22753
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21839
X-RAY DIFFRACTIONr_nbtor_other0.0890.21868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2356
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7310.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.226
X-RAY DIFFRACTIONr_mcbond_it0.9831.52223
X-RAY DIFFRACTIONr_mcbond_other0.2311.5914
X-RAY DIFFRACTIONr_mcangle_it1.47223462
X-RAY DIFFRACTIONr_scbond_it2.46431603
X-RAY DIFFRACTIONr_scangle_it3.6254.51378
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 262 -
Rwork0.178 5169 -
obs--100 %

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