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- PDB-7q9c: Peptide RLSAKP in complex with human cathepsin V C25A mutant -

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Basic information

Entry
Database: PDB / ID: 7q9c
TitlePeptide RLSAKP in complex with human cathepsin V C25A mutant
Components
  • Human cathepsin V
  • RLSAKP Peptide
KeywordsHYDROLASE / CathepsinV / Peptidyl substrate
Function / homologytrifluoroacetic acid
Function and homology information
Biological speciesHomo sapiens (human)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Human cathepsin V
BA: Human cathepsin V
PAA: RLSAKP Peptide
PAC: RLSAKP Peptide
PBA: RLSAKP Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27428
Polymers50,1345
Non-polymers2,14023
Water8,827490
1
AA: Human cathepsin V
PAA: RLSAKP Peptide
PAC: RLSAKP Peptide
hetero molecules


  • defined by author
  • 26.6 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)26,62717
Polymers25,4163
Non-polymers1,21114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BA: Human cathepsin V
PBA: RLSAKP Peptide
hetero molecules


  • defined by author
  • 25.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)25,64711
Polymers24,7192
Non-polymers9299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.10, 94.10, 124.75
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-405-

HOH

21AA-446-

HOH

31AA-651-

HOH

41BA-811-

HOH

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Components

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

#1: Protein Human cathepsin V


Mass: 24021.936 Da / Num. of mol.: 2 / Mutation: C25A,N179Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus)
#2: Protein/peptide RLSAKP Peptide


Mass: 696.863 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 513 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2HF3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 77 % MPD, 23 % of 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: 1.32→50 Å / Num. obs: 131146 / % possible obs: 99.8 % / Redundancy: 11.9 % / CC1/2: 1 / Net I/σ(I): 18.1
Reflection shellResolution: 1.32→1.4 Å / Num. unique obs: 20692 / CC1/2: 0.26

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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→47.05 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.8254 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 110246 100 %NONE
Rwork0.1837 110243 --
all0.1837 ---
obs0.1837 110243 100 %-
Solvent computationSolvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 37.16 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso max: 113.21 Å2 / Biso mean: 24.9 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 140 490 4087
LS refinement shellResolution: 1.4→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3224 5443 100 %
Rwork0.2982 5443 -
all-5443 -
obs-5443 1 %

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