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- PDB-7qgw: Sulfonated Calpeptin is a promising drug candidate against SARS-C... -

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Basic information

Entry
Database: PDB / ID: 7qgw
TitleSulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections
ComponentsCathepsin L2
KeywordsHYDROLASE / cathepsin / inhibitor
Function / homology
Function and homology information


cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / cysteine-type peptidase activity / MHC class II antigen presentation / Degradation of the extracellular matrix ...cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / cysteine-type peptidase activity / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Calpeptin / Cathepsin L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLoboda, J. / Karnicar, K. / Lindic, N. / Usenik, A. / Lieske, J. / Meents, A. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Turk, D.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research Agency Slovenia
CitationJournal: Commun Biol / Year: 2023
Title: Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.
Authors: Reinke, P.Y.A. / de Souza, E.E. / Gunther, S. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Herrmann, A. / Rahmani Mashhour, A. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. ...Authors: Reinke, P.Y.A. / de Souza, E.E. / Gunther, S. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Herrmann, A. / Rahmani Mashhour, A. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / Botosso, V.F. / Santelli, G.M.M. / Kapronezai, J. / de Araujo, M.V. / Silva-Pereira, T.T. / Filho, A.F.S. / Tavares, M.S. / Florez-Alvarez, L. / de Oliveira, D.B.L. / Durigon, E.L. / Giaretta, P.R. / Heinemann, M.B. / Hauser, M. / Seychell, B. / Bohler, H. / Rut, W. / Drag, M. / Beck, T. / Cox, R. / Chapman, H.N. / Betzel, C. / Brehm, W. / Hinrichs, W. / Ebert, G. / Latham, S.L. / Guimaraes, A.M.S. / Turk, D. / Wrenger, C. / Meents, A.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L2
B: Cathepsin L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,19321
Polymers48,1082
Non-polymers2,08519
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-111 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.24, 94.24, 126.96
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-503-

GOL

21A-725-

HOH

31A-725-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cathepsin L2 / Cathepsin U / Cathepsin V


Mass: 24054.000 Da / Num. of mol.: 2 / Mutation: N108Q, N179Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSV, CATL2, CTSL2, CTSU, UNQ268/PRO305 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: O60911, cathepsin V

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Non-polymers , 5 types, 699 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-RN2 / Calpeptin


Mass: 364.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H32N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 77 % MPD, 23 % of 60 mM TRIS, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 139006 / % possible obs: 99.9 % / Redundancy: 23.7 % / CC1/2: 1 / Net I/σ(I): 32.94
Reflection shellResolution: 1.303→1.35 Å / Num. unique obs: 13653 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
MAIN2021refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FH0

1fh0


Resolution: 1.3→47.12 Å / Cor.coef. Fo:Fc: 0.9004 / Cor.coef. Fo:Fc free: 0.8602 / SU B: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.6 / Stereochemistry target values: ML
Details: Free kick ML target function uses all data for estimating phase errors
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 138987 100 %Rkick
Rwork0.1718 138983 --
all0.1718 ---
obs0.1718 138983 100 %-
Solvent computationVDW probe radii: 1.4 Å / Solvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 29.21 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 1.42 Å2 / Biso mean: 0.54 Å2 / Biso min: 0.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 134 680 4194
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2775 6775 100 %
Rwork0.2454 6775 -
all-6775 -
obs-6775 1 %

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