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- PDB-1nqc: Crystal structures of Cathepsin S inhibitor complexes -

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Basic information

Entry
Database: PDB / ID: 1nqc
TitleCrystal structures of Cathepsin S inhibitor complexes
ComponentsCathepsin S
KeywordsHYDROLASE / Antigen presentation / binding specificity / cysteine proteases / inhibitor complexes / structure-based design / structural plasticity
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 / : / adaptive immune response / ficolin-1-rich granule lumen / 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
Chem-C4P / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Menard, R. ...Pauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Menard, R. / Cygler, M. / Rath, V.L.
CitationJournal: Biochemistry / Year: 2003
Title: Specificity determinants of human cathepsin s revealed by crystal structures of complexes.
Authors: Pauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Seddon, A.P. / Menard, R. / Cygler, M. / Rath, V.L.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4772
Polymers24,0211
Non-polymers4561
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.9, 76.5, 101.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin S


Mass: 24020.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-C4P / N-[(1R)-2-(BENZYLSULFANYL)-1-FORMYLETHYL]-N-(MORPHOLIN-4-YLCARBONYL)-L-PHENYLALANINAMIDE / MORPHOLINE-4-CARBOXYLIC ACID [1-(2-BENZYLSULFANYL-1-FORMYL-ETHYLCARBAMOYL)-2-PHENYL-ETHYL]-AMIDE


Mass: 455.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.62 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium Acetate, Ammonium Sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110.8 mg/mlprotein1drop
20.125 Msodium acetate1droppH5.5
31.5 Mammonium sulfate1drop
410 %methyl pentanediol1drop
51 %MPD1drop
60.1 Msodium acetate1reservoirpH5.5
71.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2001
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 207895 / Num. obs: 207486 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.148 / Net I/σ(I): 6.4
Reflection shellResolution: 1.8→1.83 Å / Rsym value: 0.535 / % possible all: 50.5
Reflection
*PLUS
Num. obs: 25170 / Num. measured all: 207486 / Rmerge(I) obs: 0.148

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Processing

Software
NameClassification
Adxvdata processing
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Search model consists of a polyalanine homolgy model of cathepsin S constructed from cathepsin K (PDB code 1atk) and Cathepsin L from the procathepsin L (PDB code 1cj1)

1atk

1cj1


Resolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 1184 RANDOM
Rwork0.199 --
all-24541 -
obs-24541 -
Refine analyzeLuzzati coordinate error obs: 0.02 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 32 245 1964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.86
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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