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- PDB-5qc4: Crystal structure of human Cathepsin-S with bound ligand -

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Basic information

Entry
Database: PDB / ID: 5qc4
TitleCrystal structure of human Cathepsin-S with bound ligand
ComponentsCathepsin S
KeywordsHYDROLASE / D3R / Cathepsin S / Ligand Docking
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 / phagocytic vesicle / laminin binding / collagen binding / MHC class II antigen presentation / 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 / ficolin-1-rich granule lumen / adaptive immune response / 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-BC7 / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
Model detailsStructures re-refined for D3R docking challenge
AuthorsBembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Thioether acetamides as P3 binding elements for tetrahydropyrido-pyrazole cathepsin S inhibitors.
Authors: Wiener, D.K. / Lee-Dutra, A. / Bembenek, S. / Nguyen, S. / Thurmond, R.L. / Sun, S. / Karlsson, L. / Grice, C.A. / Jones, T.K. / Edwards, J.P.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionDec 20, 2017ID: 3KWN
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 2.0Jun 6, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Refinement description / Structure summary
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / refine / refine_hist / reflns_shell
Item: _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_mon_id ..._atom_site.occupancy / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine_hist.d_res_low / _reflns_shell.pdbx_diffrn_id
Revision 2.1Feb 10, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 2.2Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 2.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)50,3374
Polymers49,0332
Non-polymers1,3042
Water9,764542
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1682
Polymers24,5161
Non-polymers6521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1682
Polymers24,5161
Non-polymers6521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.020, 52.970, 58.580
Angle α, β, γ (deg.)70.75, 71.79, 73.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cathepsin S


Mass: 24516.471 Da / Num. of mol.: 2 / Mutation: C139S
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-BC7 / 2-[5-[5-ethanoyl-1-[(2~{R})-2-oxidanyl-3-[4-(2-oxidanylpropan-2-yl)piperidin-1-yl]propyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]-2-(trifluoromethyl)phenyl]sulfanyl-1-pyrrolidin-1-yl-ethanone


Mass: 651.783 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H44F3N5O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 23183 / % possible obs: 94.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 5.1 / % possible all: 84.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.23data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.1 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.22 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1187 5.05 %
Rwork0.152 --
obs0.155 23498 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3405 0 90 542 4037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083593
X-RAY DIFFRACTIONf_angle_d0.9724880
X-RAY DIFFRACTIONf_dihedral_angle_d12.1992086
X-RAY DIFFRACTIONf_chiral_restr0.057488
X-RAY DIFFRACTIONf_plane_restr0.006625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.3151830.19721658X-RAY DIFFRACTION52
2.091-2.20130.23611390.18332630X-RAY DIFFRACTION84
2.2013-2.33920.21931390.17352959X-RAY DIFFRACTION94
2.3392-2.51980.27671600.18122972X-RAY DIFFRACTION95
2.5198-2.77330.24041820.18012953X-RAY DIFFRACTION96
2.7733-3.17450.23411560.15643009X-RAY DIFFRACTION96
3.1745-3.9990.18911480.12653061X-RAY DIFFRACTION97
3.999-42.1050.15091800.12363069X-RAY DIFFRACTION98

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