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- PDB-7qo2: Peptide GAKSAA in complex with human cathepsin V C25A mutant -

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Basic information

Entry
Database: PDB / ID: 7qo2
TitlePeptide GAKSAA in complex with human cathepsin V C25A mutant
Components
  • Cathepsin L2
  • EYS Peptide
  • GAKSAA 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 / 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 / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar 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
trifluoroacetic acid / Cathepsin L2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 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: To Be Published
Title: Peptide GAKSAA in complex with human cathepsin V C25A mutant
Authors: Loboda, J. / Sosnowski, P. / Tusar, L. / Vidmar, R. / Vizovisek, M. / Horvat, J. / Kosec, G. / Impens, F. / Demol, H. / Turk, B. / Gevaert, K. / Turk, D.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: GAKSAA Peptide
PAB: GAKSAA Peptide
PB: EYS Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,76817
Polymers49,6815
Non-polymers1,08812
Water7,224401
1
AA: Cathepsin L2
BA: Cathepsin L2
PAA: GAKSAA Peptide
hetero molecules


  • defined by author
  • 49.9 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)49,86615
Polymers48,7793
Non-polymers1,08812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
PAB: GAKSAA Peptide
PB: EYS Peptide


  • defined by author
  • 902 Da, 2 polymers
Theoretical massNumber of molelcules
Total (without water)9022
Polymers9022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.28, 94.28, 126.76
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-434-

HOH

21AA-597-

HOH

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Components

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Protein , 1 types, 2 molecules AABA

#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

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Protein/peptide , 2 types, 3 molecules PAAPABPB

#2: Protein/peptide GAKSAA Peptide


Mass: 504.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide EYS Peptide


Mass: 397.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 413 molecules

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


Mass: 118.174 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2HF3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 57.05 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.89429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 56232 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 15.89
Reflection shellResolution: 1.77→1.83 Å / Num. unique obs: 5437 / CC1/2: 0.605

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Processing

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

1fh0


Resolution: 1.77→47.14 Å / Cor.coef. Fo:Fc: 0.8983 / Cor.coef. Fo:Fc free: 0.8601 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 56232 100 %Rkick
Rwork0.1762 56230 --
all0.1762 ---
obs0.1762 56230 100 %-
Solvent computationSolvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 32.83 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 187.16 Å2 / Biso mean: 29 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.344 Å20 Å20 Å2
2---0.344 Å20 Å2
3---0.688 Å2
Refinement stepCycle: LAST / Resolution: 1.77→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 70 401 3934
LS refinement shellResolution: 1.77→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2983 2683 100 %
Rwork0.2676 2683 -
all-2683 -
obs-2683 1 %

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