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- PDB-7q8m: Peptide KPKKKTK in complex with human cathepsin V C25A mutant -

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Basic information

Entry
Database: PDB / ID: 7q8m
TitlePeptide KPKKKTK in complex with human cathepsin V C25A mutant
Components
  • Cathepsin L2
  • KPKKKTK Peptide
KeywordsHYDROLASE / CathepsinV / Peptidyl substrate
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 / extracellular matrix disassembly / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen ...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 / extracellular matrix disassembly / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / lysosome / serine-type endopeptidase activity / cysteine-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
trifluoroacetic acid / Cathepsin L2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLoboda, J. / Sosnowski, P. / Tusar, L. / Vidmar, R. / Vizovisek, M. / Horvat, J. / Kosec, G. / Impens, F. / Demol, H. / Turk, B. ...Loboda, J. / Sosnowski, P. / Tusar, L. / Vidmar, R. / Vizovisek, M. / Horvat, J. / Kosec, G. / Impens, F. / Demol, H. / Turk, B. / Gevaert, K. / Turk, D.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0048 Slovenia
CitationJournal: Commun Biol / Year: 2023
Title: Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins.
Authors: Tusar, L. / Loboda, J. / Impens, F. / Sosnowski, P. / Van Quickelberghe, E. / Vidmar, R. / Demol, H. / Sedeyn, K. / Saelens, X. / Vizovisek, M. / Mihelic, M. / Fonovic, M. / Horvat, J. / ...Authors: Tusar, L. / Loboda, J. / Impens, F. / Sosnowski, P. / Van Quickelberghe, E. / Vidmar, R. / Demol, H. / Sedeyn, K. / Saelens, X. / Vizovisek, M. / Mihelic, M. / Fonovic, M. / Horvat, J. / Kosec, G. / Turk, B. / Gevaert, K. / Turk, D.
History
DepositionNov 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Cathepsin L2
BA: Cathepsin L2
PA: KPKKKTK Peptide
PB: KPKKKTK Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,13314
Polymers50,0464
Non-polymers1,08710
Water7,116395
1
AA: Cathepsin L2
PA: KPKKKTK Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8089
Polymers25,0232
Non-polymers7857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BA: Cathepsin L2
PB: KPKKKTK Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3265
Polymers25,0232
Non-polymers3023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.23, 94.23, 125.61
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
11AA-570-

HOH

21AA-602-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules AABAPAPB

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


Mass: 24137.025 Da / Num. of mol.: 2 / Mutation: C25A, 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
#2: Protein/peptide KPKKKTK Peptide


Mass: 886.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 405 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2HF3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 288 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: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 79150 / % possible obs: 99.9 % / Redundancy: 24.8 % / CC1/2: 1 / Net I/σ(I): 30.17
Reflection shellResolution: 1.57→1.67 Å / Num. unique obs: 7711 / CC1/2: 0.815 / % possible all: 99.3

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Processing

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

1fh0


Resolution: 1.57→47.11 Å / Cor.coef. Fo:Fc: 0.8923 / Cor.coef. Fo:Fc free: 0.8502 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 79145 100 %R kick
Rwork0.1851 79145 --
all0.1851 ---
obs0.1851 79145 100 %-
Solvent computationSolvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 29.11 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 113.92 Å2 / Biso mean: 32.73 Å2 / Biso min: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.286 Å20 Å20 Å2
2---0.286 Å20 Å2
3---0.573 Å2
Refinement stepCycle: LAST / Resolution: 1.57→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 70 395 3929
LS refinement shellResolution: 1.57→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2872 3810 100 %
Rwork0.2478 3810 -
all-3810 -
obs-3810 1 %

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