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- PDB-3s3q: Structure of cathepsin B1 from Schistosoma mansoni in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3s3q
TitleStructure of cathepsin B1 from Schistosoma mansoni in complex with K11017 inhibitor
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / peptidase / digestive tract / HYDROLASE-HYDROLASE INHIBITOR complex
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
ACETATE ION / Chem-C1P / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsRezacova, P. / Jilkova, A. / Brynda, J. / Horn, M. / Mares, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for Inhibition of Cathepsin B Drug Target from the Human Blood Fluke, Schistosoma mansoni.
Authors: Jilkova, A. / Rezacova, P. / Lepsik, M. / Horn, M. / Vachova, J. / Fanfrlik, J. / Brynda, J. / McKerrow, J.H. / Caffrey, C.R. / Mares, M.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1554
Polymers28,5071
Non-polymers6483
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.092, 79.528, 90.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Fragment: UNP residues 87-340 / Mutation: T168A, T283A
Source method: isolated from a genetically manipulated source
Details: zeocin resistance / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: cb1.1, Smp_103610 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8MNY2, cathepsin B
#2: Chemical ChemComp-C1P / N~2~-(morpholin-4-ylcarbonyl)-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-leucinamide / K11017, bound form


Mass: 529.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N3O5S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: reservoir: 0.2 M Ammonium acetate pH 6.2, 0.1 M Na citrate, 30%(v/w) PEG 1500, protein buffer and concentration: 10 mM Na acetate, pH 5.5, Cpr = 2.5 mg/ml, protein: reservoir: 1:1, VAPOR ...Details: reservoir: 0.2 M Ammonium acetate pH 6.2, 0.1 M Na citrate, 30%(v/w) PEG 1500, protein buffer and concentration: 10 mM Na acetate, pH 5.5, Cpr = 2.5 mg/ml, protein: reservoir: 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2009 / Details: mirrors
RadiationMonochromator: Si111 double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 22940 / Num. obs: 22894 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1134 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-3000data collection
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
REFMAC5.3.0037phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3QSD

3qsd


Resolution: 1.8→29.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.333 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 1162 5.1 %RANDOM
Rwork0.16614 ---
all0.176 21744 --
obs0.16958 21548 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.087 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 45 536 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9632950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33724.18498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3111512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21256
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21477
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.280
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.51340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97622092
X-RAY DIFFRACTIONr_scbond_it1.743980
X-RAY DIFFRACTIONr_scangle_it2.6044.5846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 83 -
Rwork0.233 1560 -
obs--97.74 %

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