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- PDB-7q9h: Peptide LLKAVAEKQ in complex with human cathepsin V C25A mutant -

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Basic information

Entry
Database: PDB / ID: 7q9h
TitlePeptide LLKAVAEKQ in complex with human cathepsin V C25A mutant
Components
  • Cathepsin L2
  • LLKAVAEKQ 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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 12, 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
PAA: LLKAVAEKQ Peptide
PAC: LLKAVAEKQ Peptide
PB: LLKAVAEKQ Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,54921
Polymers51,1205
Non-polymers1,43016
Water9,170509
1
AA: Cathepsin L2
PAA: LLKAVAEKQ Peptide
PAC: LLKAVAEKQ Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,71811
Polymers26,0723
Non-polymers6458
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BA: Cathepsin L2
PB: LLKAVAEKQ Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,83210
Polymers25,0472
Non-polymers7848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.51, 94.51, 124.78
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-404-

HOH

21AA-410-

HOH

31AA-415-

HOH

41AA-661-

HOH

51BA-779-

HOH

61BA-809-

HOH

71BA-809-

HOH

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Components

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Protein / Protein/peptide , 2 types, 5 molecules AABAPAAPACPB

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


Mass: 24021.936 Da / Num. of mol.: 2
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 LLKAVAEKQ Peptide


Mass: 1025.265 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 525 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 55.99 %
Crystal growTemperature: 298 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 141670 / % possible obs: 99.5 % / Redundancy: 13.51 % / CC1/2: 1 / Net I/σ(I): 17.18
Reflection shellResolution: 1.29→1.37 Å / Num. unique obs: 22222 / CC1/2: 0.356

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Processing

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

1fh0


Resolution: 1.4→47.26 Å / Cor.coef. Fo:Fc: 0.8851 / Cor.coef. Fo:Fc free: 0.8418 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 111094 100 %NONE
Rwork0.1823 111094 --
all0.1823 ---
obs0.1823 111094 100 %-
Solvent computationSolvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 33.2 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 25.26 Å2 / Biso mean: 25.26 Å2 / Biso min: 25.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.033 Å20 Å20 Å2
2--0.033 Å20 Å2
3----0.067 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 90 509 4070
LS refinement shellResolution: 1.4→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2955 5465 100.02 %
Rwork0.2647 5464 -
all-5464 -
obs-5464 1 %

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