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- PDB-2ft2: Human Cathepsin S with Inhibitor CRA-29728 -

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Basic information

Entry
Database: PDB / ID: 2ft2
TitleHuman Cathepsin S with Inhibitor CRA-29728
Componentscathepsin S
KeywordsTRANSFERASE / cysteine protease / proteinase / 29728
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 / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / 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 / adaptive immune response / ficolin-1-rich granule lumen / 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-C28 / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSomoza, J.R.
CitationJournal: To be Published
Title: Human Cathepsin S with Inhibitor CRA-29728
Authors: Somoza, J.R.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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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)50,9774
Polymers50,0122
Non-polymers9652
Water4,900272
1
A: cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4892
Polymers25,0061
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4892
Polymers25,0061
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.759, 85.759, 151.150
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number91
Space group name H-MP4122
DetailsThe biologically-relevant is probably the monomer. A monomer would be one half of the asymmetric unit.

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Components

#1: Protein cathepsin S /


Mass: 25006.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-C28 / N-[1-(AMINOMETHYL)CYCLOPROPYL]-3-(MORPHOLIN-4-YLSULFONYL)-N~2~-[(1S)-2,2,2-TRIFLUORO-1-(4-FLUOROPHENYL)ETHYL]-L-ALANINAMIDE


Mass: 482.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26F4N4O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 22.5%-30% PEG 8K, 0.1 M sodium citrate (pH 5.0), 0.2 M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 62673 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.094 / Χ2: 1.183
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.65 / Num. unique obs: 2992 / Χ2: 0.811 / % possible all: 96.5

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Phasing

Phasing MRRfactor: 0.383 / Cor.coef. Fo:Fc: 0.647
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.2phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.44 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 6059 9.7 %RANDOM
Rwork0.201 ---
obs0.202 59856 95.4 %-
Displacement parametersBiso mean: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.276 Å20 Å20 Å2
2---0.276 Å20 Å2
3---0.552 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 64 272 3686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2cra2.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param

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