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- PDB-2r9n: Cathepsin S complexed with Compound 26 -

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Basic information

Entry
Database: PDB / ID: 2r9n
TitleCathepsin S complexed with Compound 26
ComponentsCathepsin S
KeywordsHYDROLASE / CATHEPSIN / PROTEASE / Glycoprotein / Lysosome / Polymorphism / Thiol protease / Zymogen
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 / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / 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-Y14 / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWard, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. ...Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. / Hrapchak, M. / DeTuri, M. / White, A. / Crane, K.M. / White, D.M. / Wang, Y. / Hao, M.-H. / Grygon, C.A. / Labadia, M.E. / Wildeson, J. / Freeman, D. / Nelson, R. / Capolino, A. / Peterson, J.D. / Raymond, E.L. / Brown, M.L. / Spero, D.M.
CitationJournal: to be published
Title: Design and Synthesis of Reversible Inhibitors of Cathepsin S: alpha,alpha-Disubstitution at the P1 Residue Provides Potent Inhibitors in Cellular Assays and In Vivo Models of Antigen Presentation
Authors: Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. / Hrapchak, M. / DeTuri, M. / White, A. / Crane, K. ...Authors: Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. / Hrapchak, M. / DeTuri, M. / White, A. / Crane, K.M. / White, D.M. / Wang, Y. / Hao, M.-H. / Grygon, C.A. / Labadia, M.E. / Wildeson, J. / Freeman, D. / Nelson, R. / Capolino, A. / Peterson, J.D. / Raymond, E.L. / Brown, M.L. / Spero, D.M.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)50,3314
Polymers49,3952
Non-polymers9352
Water5,621312
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1652
Polymers24,6981
Non-polymers4681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1652
Polymers24,6981
Non-polymers4681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.296, 85.296, 149.961
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-376-

HOH

21B-390-

HOH

31B-433-

HOH

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Components

#1: Protein Cathepsin S


Mass: 24697.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Escherichia coli (E. coli) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-Y14 / N-[(1S)-2-{[(3S)-1-benzyl-3-cyanopyrrolidin-3-yl]amino}-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide


Mass: 467.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H37N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM NaOAc, 18-35% PEG MME (500-8000), 2 M (NH4)2SO4 with or without 15% glycerol, pH 4.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: Osmic focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38189 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rsym value: 0.081

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Processing

Software
NameVersionClassificationNB
X-PLOR98.1refinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CNSrefinement
RefinementStarting model: pdb entry 1MS6

1ms6


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22 1965 random
Rwork0.183 --
obs-38137 -
Displacement parametersBiso mean: 21.156 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 68 312 3744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_improper_angle_d0.79

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