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- PDB-1ms6: Dipeptide Nitrile Inhibitor Bound to Cathepsin S. -

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Basic information

Entry
Database: PDB / ID: 1ms6
TitleDipeptide Nitrile Inhibitor Bound to Cathepsin S.
ComponentsCathepsin S
KeywordsHYDROLASE / cathepsin / protease
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-BLN / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWard, Y.D. / Thomson, D.S. / Frye, L.L. / Cywin, C.L. / Morwick, T. / Emmanuel, M.J. / Zindell, R. / McNeil, D. / Bekkali, Y. / Giradot, M. ...Ward, Y.D. / Thomson, D.S. / Frye, L.L. / Cywin, C.L. / Morwick, T. / Emmanuel, M.J. / Zindell, R. / McNeil, D. / Bekkali, Y. / Giradot, M. / Hrapchak, M. / DeTuri, M. / Crane, K. / White, D. / Pav, S. / Wang, Y. / Hao, M.H. / Grygon, C.A. / Labadia, M.E. / Freeman, D.M. / Davidson, W. / Hopkins, J.L. / Brown, M.L. / Spero, D.M.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Design and synthesis of dipeptide nitriles as reversible and potent Cathepsin S inhibitors
Authors: Ward, Y.D. / Thomson, D.S. / Frye, L.L. / Cywin, C.L. / Morwick, T. / Emmanuel, M.J. / Zindell, R. / McNeil, D. / Bekkali, Y. / Giradot, M. / Hrapchak, M. / DeTuri, M. / Crane, K. / White, D. ...Authors: Ward, Y.D. / Thomson, D.S. / Frye, L.L. / Cywin, C.L. / Morwick, T. / Emmanuel, M.J. / Zindell, R. / McNeil, D. / Bekkali, Y. / Giradot, M. / Hrapchak, M. / DeTuri, M. / Crane, K. / White, D. / Pav, S. / Wang, Y. / Hao, M.H. / Grygon, C.A. / Labadia, M.E. / Freeman, D.M. / Davidson, W. / Hopkins, J.L. / Brown, M.L. / Spero, D.M.
History
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1002
Polymers24,6981
Non-polymers4021
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.29, 85.29, 150.07
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Cathepsin S


Mass: 24697.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-BLN / MORPHOLINE-4-CARBOXYLIC ACID [1S-(2-BENZYLOXY-1R-CYANO-ETHYLCARBAMOYL)-3-METHYL-BUTYL]AMIDE


Mass: 402.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N4O4

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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

Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.6-2.0 Mammonium sulfate1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 42565
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 95.9 % / Num. measured all: 545688 / Rmerge(I) obs: 0.146

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.197 2130 RANDOM
Rwork0.155 --
all0.169 42565 -
obs0.162 42565 -
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 29 0 1714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_improper_angle_d0.77
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.77

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