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

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Basic information

Entry
Database: PDB / ID: 3qsd
TitleStructure of cathepsin B1 from Schistosoma mansoni in complex with CA074 inhibitor
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine peptidase / digestive tract / HYDROLASE-HYDROLASE INHIBITOR complex
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 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
[PROPYLAMINO-3-HYDROXY-BUTAN-1,4-DIONYL]-ISOLEUCYL-PROLINE / Chem-074 / ACETATE ION / DI(HYDROXYETHYL)ETHER / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,1175
Polymers28,5071
Non-polymers6104
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.177, 79.160, 90.610
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-074 / [PROPYLAMINO-3-HYDROXY-BUTAN-1,4-DIONYL]-ISOLEUCYL-PROLINE / CA-074 / [N-(L-3-TRANS-PROPYLCARBAMOYL-OXIRANE-2-CARBONYL)-L-ISOLEUCYL-L-PROLINE]


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 385.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H31N3O6
References: [PROPYLAMINO-3-HYDROXY-BUTAN-1,4-DIONYL]-ISOLEUCYL-PROLINE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR CA-074 HAS AN OXIRANE RING. ITS CONFIGURATION CHANGES(OPENS UP) ...THE UNBOUND FORM OF THE INHIBITOR CA-074 HAS AN OXIRANE RING. ITS CONFIGURATION CHANGES(OPENS UP) UPON BINDING TO SG OF CYS100. THIS BOUND OPEN CONFIGURATION OF THE INHIBITOR IS REPRESENTED IN 074

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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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.2M Ammonium Acetate, 0.1M Na Citrate, 30% (v/w) PEG 1500, 10mM Na Acetate pH 5.5, Cpr concentration = 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: 1.3→50 Å / Num. all: 59635 / Num. obs: 55759 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.29
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.7 / % possible all: 61.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUC

1huc


Resolution: 1.3→22.33 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.273 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15473 2805 5 %RANDOM
Rwork0.11407 ---
all0.11608 56435 --
obs0.11608 52880 93.57 %-
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: 12.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 42 472 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.9653078
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16124.216102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01215413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2961513
X-RAY DIFFRACTIONr_chiral_restr0.120.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021755
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21177
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21547
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2387
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.291
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0191.51385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.67922181
X-RAY DIFFRACTIONr_scbond_it3.40431025
X-RAY DIFFRACTIONr_scangle_it4.5014.5874
X-RAY DIFFRACTIONr_rigid_bond_restr2.03332410
X-RAY DIFFRACTIONr_sphericity_free10.0283472
X-RAY DIFFRACTIONr_sphericity_bonded5.02832177
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 144 -
Rwork0.131 2554 -
obs--62.07 %

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