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- PDB-9fzv: Structure of cathepsin B1 from Schistosoma mansoni (SmCB1) in com... -

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Basic information

Entry
Database: PDB / ID: 9fzv
TitleStructure of cathepsin B1 from Schistosoma mansoni (SmCB1) in complex with a carborane inhibitor
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE / protease / parasite / inhibitor / carborane
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis
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
: / Cathepsin B-like cysteine proteinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJilkova, A. / Fanfrlik, J. / Brynda, J. / Spiwokova, P. / Horn, M. / Holub, J. / Guetschow, M. / Mares, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation23-05083S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLUAUS23050 Czech Republic
Czech Academy of SciencesRVO 61388963 Czech Republic
CitationJournal: Inorg Chem Front / Year: 2025
Title: Fat or flat? The impact of dipole moment vectors on non-covalent interactions between aromatic tags and macromolecules.
Authors: Holub, J. / Jilkova, A. / Lemke, C. / Cianni, L. / Spiwokova, P. / Horn, M. / Breuer, C. / Leontovyc, A. / Brynda, J. / Mertlikova-Kaiserova, H. / Chanova, M. / Dos Reis Rocho, F. / ...Authors: Holub, J. / Jilkova, A. / Lemke, C. / Cianni, L. / Spiwokova, P. / Horn, M. / Breuer, C. / Leontovyc, A. / Brynda, J. / Mertlikova-Kaiserova, H. / Chanova, M. / Dos Reis Rocho, F. / Montanari, C.A. / El-Sakkary, N. / Caffrey, C.R. / Gutschow, M. / Hnyk, D. / Mares, M. / Fanfrlik, J.
History
DepositionJul 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)87,24511
Polymers85,5223
Non-polymers1,7238
Water2,108117
1
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1645
Polymers28,5071
Non-polymers6574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1024
Polymers28,5071
Non-polymers5953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9782
Polymers28,5071
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.726, 81.726, 102.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: pPICZalpha / Details (production host): zeocin resistance / Production host: Komagataella pastoris (fungus) / Variant (production host): X-33 / References: UniProt: Q8MNY2
#2: Chemical ChemComp-A1IHQ / carborane inhibitor / carborane inhibitor


Mass: 470.964 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H17B10ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 200 mM ammonium acetate, 100 mM sodium citrate, 30% PEG 1 500, 2 mM 2-mercaptoethanol, pH 6.2 c (protein)= 5 mg/mL ratio protein:reservoir = 1:1 cryocooled in reservoir solution supplemented ...Details: 200 mM ammonium acetate, 100 mM sodium citrate, 30% PEG 1 500, 2 mM 2-mercaptoethanol, pH 6.2 c (protein)= 5 mg/mL ratio protein:reservoir = 1:1 cryocooled in reservoir solution supplemented with 30% PEG 300, 1.75 mM DTT, 0.07 mM carborane inhibitor 2-oC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38651 / % possible obs: 99.8 % / Redundancy: 5.861 % / CC1/2: 0.985 / Net I/σ(I): 5.21
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.2-2.3362190.3521
2.33-2.4958860.5291
2.49-2.6954530.6941
2.69-2.9550270.8451
2.95-3.2945360.9341
3.29-3.840300.9811
3.8-4.6433720.9911
4.64-6.5326480.9921
6.53-5014800.9961

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.4 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.656 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25024 1972 5.1 %RANDOM
Rwork0.20195 ---
obs0.2044 36677 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.734 Å2
Baniso -1Baniso -2Baniso -3
1-11.13 Å20 Å20 Å2
2--11.13 Å20 Å2
3----22.26 Å2
Refinement stepCycle: 1 / Resolution: 2.2→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 122 117 6233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196354
X-RAY DIFFRACTIONr_bond_other_d0.0120.025751
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9988834
X-RAY DIFFRACTIONr_angle_other_deg3.375313426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1223.827277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2061536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1793.7493047
X-RAY DIFFRACTIONr_mcbond_other3.1753.7493046
X-RAY DIFFRACTIONr_mcangle_it4.4695.6193804
X-RAY DIFFRACTIONr_mcangle_other4.4695.6193805
X-RAY DIFFRACTIONr_scbond_it3.323.913307
X-RAY DIFFRACTIONr_scbond_other3.323.913307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8355.7634751
X-RAY DIFFRACTIONr_long_range_B_refined6.59429.3317248
X-RAY DIFFRACTIONr_long_range_B_other6.59429.3327249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 120 -
Rwork0.254 2728 -
obs--98.99 %

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