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- PDB-2g6d: Human cathepsin S mutant with vinyl sulfone inhibitor CRA-14009 -

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Basic information

Entry
Database: PDB / ID: 2g6d
TitleHuman cathepsin S mutant with vinyl sulfone inhibitor CRA-14009
Componentscathepsin S
KeywordsHYDROLASE / Papain / Cysteine protease / proteinase / 14009
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-MQQ / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSomoza, J.R.
CitationJournal: To be Published
Title: Human cathepsin S mutant with vinyl sulfone inhibitor CRA-14009
Authors: Somoza, J.R.
History
DepositionFeb 24, 2006Deposition 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: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7192
Polymers24,0771
Non-polymers6421
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.47, 85.89, 116.26
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222

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Components

#1: Protein cathepsin S


Mass: 24077.119 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-MQQ / N-[(1S)-1-[({(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}AMINO)CARBONYL]-3-(PHENYLSULFONYL)PROPYL]MORPHOLINE-4-CARBOXAMIDE


Mass: 641.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H39N3O7S2
#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: 4.12 Å3/Da / Density % sol: 70.13 %
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 280.0K

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 11532 / % possible obs: 81.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.196 / Χ2: 1.18 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 85.3 % / Rmerge(I) obs: 0.866 / Num. unique obs: 1178 / Χ2: 1.046 / % possible all: 85.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→69.08 Å / FOM work R set: 0.861 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1067 7.6 %RANDOM
Rwork0.192 ---
obs0.195 10724 76 %-
Displacement parametersBiso mean: 19.795 Å2
Baniso -1Baniso -2Baniso -3
1-2.936 Å20 Å20 Å2
2---3.653 Å20 Å2
3---0.717 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→69.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 44 78 1762
Refine LS restraintsType: c_bond_d / Dev ideal: 0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.5-2.540.381550.343394449
2.54-2.580.272580.328451509
2.58-2.630.394520.302427479
2.63-2.680.328480.291454502
2.68-2.740.255520.28448500
2.74-2.80.305490.282465514
2.8-2.860.264470.271463510
2.86-2.930.278560.241462518
2.93-3.010.245500.211459509
3.01-3.10.244480.239468516
3.1-3.20.195510.183467518
3.2-3.320.21620.169473535
3.32-3.450.237410.186488529
3.45-3.610.184500.159478528
3.61-3.80.227490.142467516
3.8-4.030.17500.124478528
4.03-4.350.169570.124482539
4.35-4.780.17460.129463509
4.78-5.470.151440.134470514
5.47-6.90.22470.171467514
6.9-500.010.209550.176433488
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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