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- PDB-5ogq: Structure of cathepsin B1 from Schistosoma mansoni in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5ogq
TitleStructure of cathepsin B1 from Schistosoma mansoni in complex with WRR391 inhibitor
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE / protease / parasite / inhibitor / vinyl sulfone
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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-9U8 / ACETATE ION / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsJilkova, A. / Rezacova, P. / Brynda, J. / Mares, M.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLO1304 Czech Republic
Czech Academy of SciencesRVO 61388963 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLH15040 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicInterBioMed LO1302 Czech Republic
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Druggable Hot Spots in the Schistosomiasis Cathepsin B1 Target Identified by Functional and Binding Mode Analysis of Potent Vinyl Sulfone Inhibitors.
Authors: Jilkova, A. / Rubesova, P. / Fanfrlik, J. / Fajtova, P. / Rezacova, P. / Brynda, J. / Lepsik, M. / Mertlikova-Kaiserova, H. / Emal, C.D. / Renslo, A.R. / Roush, W.R. / Horn, M. / Caffrey, C.R. / Mares, M.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)
B: Cathepsin B-like peptidase (C01 family)
C: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5337
Polymers85,5223
Non-polymers2,0114
Water7,963442
1
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1582
Polymers28,5071
Non-polymers6511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2173
Polymers28,5071
Non-polymers7102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1582
Polymers28,5071
Non-polymers6511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.390, 82.390, 99.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 28507.256 Da / Num. of mol.: 3 / Mutation: T168A, T283A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: cb1.1, Smp_103610 / Plasmid: pPICZalphaA / Details (production host): zeocin resistance / Production host: Pichia (fungus) / Variant (production host): X-33 / References: UniProt: Q8MNY2
#2: Chemical ChemComp-9U8 / ethyl 1-[[(2~{S})-3-(4-hydroxyphenyl)-1-oxidanylidene-1-[[(3~{S})-1-phenyl-5-pyridin-2-ylsulfonyl-pentan-3-yl]amino]propan-2-yl]carbamoyl]piperidine-4-carboxylate


Mass: 650.785 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H42N4O7S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.14 M Ammonium Acetate, 0.07 M Sodium Citrate, 21% PEG 400 c (protein) = 3.4 mg/ml ratio protein : reservoir : H2O = 2:0.5:0.5ul cryocooled in mother liquor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.063
11-K, -H, -L20.412
11-h,-k,l30.456
11K, H, -L40.068
ReflectionResolution: 1.91→38.06 Å / Num. obs: 52771 / % possible obs: 89.5 % / Redundancy: 2.799 % / Biso Wilson estimate: 31.098 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.095 / Χ2: 1.03 / Net I/σ(I): 9.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.91-1.951.4380.7990.6821490.41.12848.7
1.95-2.011.6780.7150.9930510.4670.9772.1
2.01-2.071.8360.5341.4232560.6070.70878.8
2.07-2.131.9620.4541.8232220.6350.681
2.13-2.22.0610.3542.5133720.7620.4686.2
2.2-2.282.2180.3133.1134500.8560.40192
2.28-2.362.4850.2693.9235000.9110.33996.2
2.36-2.462.8520.2294.9234630.9070.28299
2.46-2.573.3580.1946.333700.9540.231100
2.57-2.693.4450.1527.8632060.9730.18100
2.69-2.843.5560.1289.2330420.9810.15100
2.84-3.013.6070.09312.6228800.9890.109100
3.01-3.223.5990.08114.6327060.9910.09599.9
3.22-3.483.4790.0618.8625280.9950.07299.7
3.48-3.813.2270.04722.8722830.9950.05698.9
3.81-4.262.9970.04324.7220630.9960.05199.1
4.26-4.923.6480.03829.1518540.9980.04499.7
4.92-6.023.5560.04325.9115470.9980.05199
6.02-8.523.0630.03826.1511890.9970.04698.8
8.52-38.063.8140.03133.876400.9990.03596.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I07

4i07


Resolution: 1.91→38.06 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.888 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.028
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 1367 2.6 %RANDOM
Rwork0.1674 ---
obs0.1679 51402 89.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.74 Å2 / Biso mean: 29.432 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.73 Å20 Å20 Å2
2--8.73 Å20 Å2
3----17.45 Å2
Refinement stepCycle: final / Resolution: 1.91→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 142 443 6579
Biso mean--22.79 30.98 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196337
X-RAY DIFFRACTIONr_bond_other_d0.0030.025787
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9648559
X-RAY DIFFRACTIONr_angle_other_deg0.843313425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86523.827277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.736151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3411536
X-RAY DIFFRACTIONr_chiral_restr0.080.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
LS refinement shellResolution: 1.905→1.955 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 60 -
Rwork0.282 2072 -
all-2132 -
obs--48.52 %

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