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- PDB-2fye: Mutant Human Cathepsin S with irreversible inhibitor CRA-14013 -

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Basic information

Entry
Database: PDB / ID: 2fye
TitleMutant Human Cathepsin S with irreversible inhibitor CRA-14013
Componentscathepsin S preproprotein
KeywordsHYDROLASE / papain / cysteine protease / drug design / 14013
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-BCQ / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsSomoza, J.R.
CitationJournal: To be Published
Title: Mutant Human Cathepsin S with irreversible inhibitor CRA-14013
Authors: Somoza, J.R.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 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
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cathepsin S preproprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6822
Polymers24,0191
Non-polymers6631
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.58, 85.43, 116.26
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222
DetailsThe biologically-relevant unit is probably the monomer. There is one monomer/asymmetric unit.

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Components

#1: Protein cathepsin S preproprotein


Mass: 24019.082 Da / Num. of mol.: 1 / Mutation: S108R, E184K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-BCQ / N-[(1R)-1-[({[(5S)-3,5-DIMETHYL-2,5-DIHYDROISOXAZOL-4-YL]METHYL}SULFONYL)METHYL]-2-OXO-2-({(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}AMINO)ETHYL]MORPHOLINE-4-CARBOXAMIDE


Mass: 662.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H42N4O8S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 4.5
Details: Under typical crystallization conditions the reservoir contained 80 mM ammonium sulfate and 12% (w/v) polyethylene glycol 8000. This was allowed to equilibrate with a hanging drop containing ...Details: Under typical crystallization conditions the reservoir contained 80 mM ammonium sulfate and 12% (w/v) polyethylene glycol 8000. This was allowed to equilibrate with a hanging drop containing 2 microliters of the reservoir solution and 2 microliters of a 10 mg/mL protein solution in 25 mM sodium acetate (pH 4.5). , VAPOR DIFFUSION, temperature 280K

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 18684 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.124 / Χ2: 1.02 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.632 / Num. unique obs: 1913 / Χ2: 1.144 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→65.7 Å / FOM work R set: 0.853 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1705 8.3 %RANDOM
Rwork0.194 ---
obs0.208 17532 85.5 %-
Displacement parametersBiso mean: 21.927 Å2
Baniso -1Baniso -2Baniso -3
1-2.059 Å20 Å20 Å2
2---1.951 Å20 Å2
3----0.108 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→65.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 45 78 1763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 34

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.220.38430.324448491
2.22-2.240.349430.316444487
2.24-2.270.351490.3436485
2.27-2.290.228390.297444483
2.29-2.320.332570.29423480
2.32-2.350.292460.288463509
2.35-2.380.268510.265446497
2.38-2.410.291450.268469514
2.41-2.440.299530.261479532
2.44-2.470.3530.275446499
2.47-2.510.303420.254477519
2.51-2.540.368380.263461499
2.54-2.580.308510.239496547
2.58-2.630.286470.247448495
2.63-2.670.206490.216484533
2.67-2.720.262460.222470516
2.72-2.770.213450.215472517
2.77-2.830.248580.227471529
2.83-2.890.227450.217465510
2.89-2.960.232430.217498541
2.96-3.030.244600.206471531
3.03-3.110.287530.183468521
3.11-3.20.23560.175481537
3.2-3.310.244510.176488539
3.31-3.430.223480.162485533
3.43-3.560.174560.148474530
3.56-3.730.153470.143477524
3.73-3.920.141560.133483539
3.92-4.170.106450.118474519
4.17-4.490.128600.129470530
4.49-4.940.125600.123456516
4.94-5.660.127630.146457520
5.66-7.130.261390.173475514
7.13-500.010.162680.175428496
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2parhcsdx_from_mary.pro
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param

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