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- PDB-6yi7: Structure of cathepsin B1 from Schistosoma mansoni (SmCB1) in com... -

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Basic information

Entry
Database: PDB / ID: 6yi7
TitleStructure of cathepsin B1 from Schistosoma mansoni (SmCB1) in complex with an azanitrile inhibitor
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE / cysteine protease / parasite / inhibitor / azanitrile
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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
ACETATE ION / Chem-ORW / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsJilkova, A. / Rezacova, P. / Pachl, P. / Fanfrlik, J. / Rubesova, P. / Guetschow, M. / Mares, M.
Funding support Czech Republic, European Union, 3items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLTAUSA19109 Czech Republic
European Regional Development FundChemBioDrug CZ.02.1.01/0.0/0.0/16_019/0000729European Union
Czech Academy of SciencesRVO 61388963 Czech Republic
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Azanitrile Inhibitors of the SmCB1 Protease Target Are Lethal to Schistosoma mansoni : Structural and Mechanistic Insights into Chemotype Reactivity.
Authors: Jilkova, A. / Horn, M. / Fanfrlik, J. / Kuppers, J. / Pachl, P. / Rezacova, P. / Lepsik, M. / Fajtova, P. / Rubesova, P. / Chanova, M. / Caffrey, C.R. / Gutschow, M. / Mares, M.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9594
Polymers28,5071
Non-polymers4523
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-1 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.934, 78.965, 89.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin B-like peptidase (C01 family) / Cathepsin B1 isotype 1


Mass: 28507.256 Da / Num. of mol.: 1 / Mutation: T168A, T283A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: cb1.1, Smp_103610 / Plasmid: pPICZalpha / Details (production host): zeocin resistance / Production host: Komagataella pastoris (fungus) / Variant (production host): X-33 / References: UniProt: Q8MNY2
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ORW / 1-[(2~{S})-1-[[iminomethyl(methyl)amino]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-(phenylmethyl)urea


Mass: 333.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 180 mM ammonium acetate, 80 mM sodium citrate, 27% PEG 1 500, pH 6.1 c (protein)= 4 mg/mL ratio protein:reservoir = 1:1 cryocooled in mother liquor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.29→44.98 Å / Num. obs: 58937 / % possible obs: 98.9 % / Redundancy: 3.24 % / Biso Wilson estimate: 16.587 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.062 / Χ2: 0.878 / Net I/σ(I): 13.53 / Num. measured all: 190961
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.29-1.373.2760.4042.7630630950393510.7850.48398.4
1.37-1.473.1350.3023.5327805893688700.8730.36499.3
1.47-1.583.3420.2015.4627753835183040.9460.23999.4
1.58-1.733.1680.1288.0924191770076350.9760.15499.2
1.73-1.943.3540.08213.0523433701669870.990.09799.6
1.94-2.243.180.04821.319340618360820.9960.05898.4
2.24-2.743.3410.03628.0717650530752830.9980.04399.5
2.74-3.873.1660.02438.3812868415840650.9990.02897.8
3.87-44.983.0890.02145.767291244023600.9990.02696.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S3Q

3s3q


Resolution: 1.29→44.98 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1497 / WRfactor Rwork: 0.1141 / FOM work R set: 0.8969 / SU B: 1.697 / SU ML: 0.032 / SU R Cruickshank DPI: 0.042 / SU Rfree: 0.0427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1571 1147 1.9 %RANDOM
Rwork0.1206 ---
obs0.1213 57789 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.41 Å2 / Biso mean: 14.74 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0 Å2
2--0.19 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.29→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 32 408 2438
Biso mean--27.55 27.8 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192167
X-RAY DIFFRACTIONr_bond_other_d0.0010.022000
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9562938
X-RAY DIFFRACTIONr_angle_other_deg0.87534649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38623.83899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41515382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2321514
X-RAY DIFFRACTIONr_chiral_restr0.1080.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_rigid_bond_restr2.99134167
X-RAY DIFFRACTIONr_sphericity_free31.025580
X-RAY DIFFRACTIONr_sphericity_bonded9.92754426
LS refinement shellResolution: 1.293→1.327 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 82 -
Rwork0.189 4144 -
all-4226 -
obs--97.15 %

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