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- PDB-2f1g: Cathepsin S in complex with non-covalent 2-(Benzoxazol-2-ylamino)... -

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Basic information

Entry
Database: PDB / ID: 2f1g
TitleCathepsin S in complex with non-covalent 2-(Benzoxazol-2-ylamino)-acetamide
ComponentsCathepsin S
KeywordsHYDROLASE / Cathepsin S / noncovalent / inhibition / 2-(Benzooxazol-2-ylamino) acetamides
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 / fibronectin binding / antigen processing and presentation / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / positive regulation of apoptotic signaling pathway / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar 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 / serine-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-GNF / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSpraggon, G. / Hornsby, M. / Lesley, S.A. / Tully, D.C. / Harris, J.L. / Karenewsky, D.S. / Kulathila, R. / Clark, K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Synthesis and evaluation of arylaminoethyl amides as noncovalent inhibitors of cathepsin S. Part 3: Heterocyclic P3.
Authors: Tully, D.C. / Liu, H. / Alper, P.B. / Chatterjee, A.K. / Epple, R. / Roberts, M.J. / Williams, J.A. / Nguyen, K.T. / Woodmansee, D.H. / Tumanut, C. / Li, J. / Spraggon, G. / Chang, J. / ...Authors: Tully, D.C. / Liu, H. / Alper, P.B. / Chatterjee, A.K. / Epple, R. / Roberts, M.J. / Williams, J.A. / Nguyen, K.T. / Woodmansee, D.H. / Tumanut, C. / Li, J. / Spraggon, G. / Chang, J. / Tuntland, T. / Harris, J.L. / Karanewsky, D.S.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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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)49,7485
Polymers48,7832
Non-polymers9653
Water5,873326
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8282
Polymers24,3911
Non-polymers4371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9203
Polymers24,3911
Non-polymers5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.250, 85.250, 151.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Detailsthe biological unit is a monomer

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Components

#1: Protein Cathepsin S /


Mass: 24391.393 Da / Num. of mol.: 2 / Fragment: Cathepsin S
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-GNF / N~2~-1,3-BENZOXAZOL-2-YL-3-CYCLOHEXYL-N-{2-[(4-METHOXYPHENYL)AMINO]ETHYL}-L-ALANINAMIDE


Mass: 436.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32N4O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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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: 56.42 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% Peg-8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→84.51 Å / Num. all: 39331 / Num. obs: 39331 / % possible obs: 92.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 14.31
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.75 / Num. unique all: 3764 / Rsym value: 0.737 / % possible all: 85.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→84.51 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.189 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Electron Density for the methoxyphenyl amino group, modeled in the P' site is largely absent.
RfactorNum. reflection% reflectionSelection details
Rfree0.23033 2119 5.1 %RANDOM
Rwork0.18914 ---
all0.19125 39331 --
obs0.19125 39331 92.44 %-
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: 18.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 70 326 3792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223585
X-RAY DIFFRACTIONr_bond_other_d0.0010.023062
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9644853
X-RAY DIFFRACTIONr_angle_other_deg0.7637171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25824.233163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12515570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1441516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024053
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02765
X-RAY DIFFRACTIONr_nbd_refined0.1990.2788
X-RAY DIFFRACTIONr_nbd_other0.180.23425
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21851
X-RAY DIFFRACTIONr_nbtor_other0.0870.21998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2303
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.220
X-RAY DIFFRACTIONr_mcbond_it1.37322772
X-RAY DIFFRACTIONr_mcbond_other0.2852930
X-RAY DIFFRACTIONr_mcangle_it1.733470
X-RAY DIFFRACTIONr_scbond_it3.40851752
X-RAY DIFFRACTIONr_scangle_it4.61481379
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 135 -
Rwork0.253 2630 -
obs--85.21 %

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