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- PDB-3s3r: Structure of cathepsin B1 from Schistosoma mansoni in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3s3r
TitleStructure of cathepsin B1 from Schistosoma mansoni in complex with K11777 inhibitor
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
MePip-Phe-HphVSPh / Chem-0IW / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.64 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 1.2Dec 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)87,2526
Polymers85,5223
Non-polymers1,7303
Water1,18966
1
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0842
Polymers28,5071
Non-polymers5771
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)29,0842
Polymers28,5071
Non-polymers5771
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)29,0842
Polymers28,5071
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.633, 103.121, 100.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A71 - 325
2116B71 - 325
3116C71 - 325

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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 / Fragment: UNP residues 87-340 / Mutation: T168A, T283A
Source method: isolated from a genetically manipulated source
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-0IW / Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide / APC-3316, bound form / 4-Methylpiperazine-1-carboxylic acid [1-[(3-benzenesulfonyl-1-phenethylallyl)carbamoyl]-2-phenylethyl]amide, bound form


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 576.749 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H40N4O4S / References: MePip-Phe-HphVSPh
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsLIGAND 0IW HAD A DOUBLE BOND BETWEEN ATOMS C11 AND C21 WHICH OPENS UP TO FORM A LINK WITH THE CYS 100

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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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: reservoir: 0.2 M Ammonium Acetate pH6.2, 0.1 M Na Citrate, 30% PEG 1500, protein buffer and concentration: 10 mM Na-acetate pH 5.5, Cpr = 6 mg/ml, protein: reservoir = 1:1, VAPOR DIFFUSION, ...Details: reservoir: 0.2 M Ammonium Acetate pH6.2, 0.1 M Na Citrate, 30% PEG 1500, protein buffer and concentration: 10 mM Na-acetate pH 5.5, Cpr = 6 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: 2.5→50 Å / Num. all: 24266 / Num. obs: 24218 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 69.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.7
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.85 / Num. unique all: 1184 / % possible all: 99.5

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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: 2.64→36.32 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 29.377 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27142 1236 5.1 %RANDOM
Rwork0.20462 ---
obs0.20815 22916 98.83 %-
all-23187 --
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: 41.508 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.64→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5953 0 123 66 6142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9618458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7423.759274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.835151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3631536
X-RAY DIFFRACTIONr_chiral_restr0.0920.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024801
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22877
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24229
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3481.53857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.58826002
X-RAY DIFFRACTIONr_scbond_it0.93732860
X-RAY DIFFRACTIONr_scangle_it1.4914.52455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1954 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.525
loose positional0.470
loose positional0.470
loose thermal1.6510
loose thermal1.390.01
loose thermal1.510
LS refinement shellResolution: 2.637→2.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 76 -
Rwork0.291 1432 -
obs--85.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.471-0.34731.12024.05533.55399.8768-0.2744-0.23440.27960.4096-0.0062-0.05210.2418-0.36580.2805-0.0003-0.0261-0.0437-0.14650.03850.0761-0.767-10.029-1.922
23.54462.53636.284857.29624.216318.7834-0.4383-1.5750.01882.1163-1.35232.46150.8256-2.78151.79070.24110.02260.14580.511-0.15780.2999-11.794-10.8481.463
33.18540.13670.11333.73741.95435.97390.11960.0874-0.21040.0419-0.22510.37031.048-1.02960.10560.0977-0.1765-0.00570.09890.00390.0551-9.118-16.722-13.656
43.0227-1.3278-0.17324.74910.29385.9543-0.1430.0701-0.32560.27330.00080.33691.3517-0.57540.14220.34-0.14970.0149-0.02050.04120.0132-5.846-20.843-8.977
54.2438-1.6685-0.43042.79150.941410.5859-0.0698-0.1070.3953-0.09490.0606-0.3071-0.16450.80390.0091-0.1626-0.0763-0.0453-0.17720.05410.16727.128-6.597-9.325
61.72080.83910.89264.37640.0576.7059-0.07310.22680.30620.1862-0.0867-0.72440.04511.16550.1597-0.09130.0126-0.07830.05960.08580.234111.864-8.353-8.12
74.8594-0.82310.34484.39450.38866.7666-0.03240.12840.6147-0.0227-0.1011-0.634-0.18490.46330.1335-0.0547-0.0265-0.0254-0.0880.04660.08126.609-6.083-8.326
83.2936-1.2302-1.72323.21350.23694.9353-0.5644-0.5416-0.16180.3470.03720.01930.70060.02620.52710.14280.1548-0.1070.2165-0.11720.0649-0.262-11.75331.94
952.23598.179547.643928.34757.337243.4561-2.86163.2551-2.99893.23352.1982-3.55372.6999-4.30870.66340.69470.6233-0.03010.5777-0.54350.3515.155-22.17738.422
104.65441.7106-1.03250.996-1.94049.8582-0.36910.0113-0.0947-0.22430.0756-0.3391.12830.87520.29350.29570.3993-0.0630.2312-0.12670.09149.546-16.85319.95
114.5426-0.8824-0.30972.5878-0.13966.0929-0.1868-0.28660.37020.2589-0.0569-0.3490.46850.98220.24360.16690.2703-0.12560.3197-0.1240.12199.716-10.42826.194
122.5276-0.47830.31490.20570.99199.6382-0.20090.05220.3165-0.1326-0.07530.227-0.4616-0.43650.27610.05190.2059-0.10310.1695-0.18660.1261-6.119-3.32923.007
131.2042-0.2183-0.80430.740.93376.57780.0266-0.02930.4188-0.0793-0.09140.2678-0.628-0.71280.06480.12970.2725-0.15390.2728-0.16680.176-10.246-3.09924.781
142.44340.72390.87825.96820.98426.578-0.1855-0.31230.2143-0.0725-0.17830.12320.2433-0.75570.36380.04890.1524-0.04260.2028-0.1610.0449-5.899-6.9325.684
156.3506-0.62854.58093.3851-3.248611.24370.04590.19720.05470.0369-0.4403-0.10160.32820.52680.39450.00170.05530.08-0.07320.01370.02350.891-10.609-35.227
168.8245-1.51622.98044.3376-5.328311.6794-1.3532-0.56711.06340.3917-0.0286-0.3046-2.3999-0.21021.38190.3131-0.0454-0.21580.01010.0880.34160.7650.283-41.383
178.5506-2.09825.83361.68981.523615.4678-1.2152-0.00982.2591-0.44210.2246-0.1081-1.82830.60020.99070.1983-0.085-0.21410.09390.01940.5298-0.434-0.109-43.736
188.009-0.48413.80664.12530.42098.8849-0.8623-0.41891.1915-0.1803-0.00630.19-0.8633-0.40120.86850.16840.088-0.0680.1048-0.0080.1147-3.955-2.956-41.592
197.5481.03437.75395.2951.792714.94680.13910.4748-0.3847-0.5652-0.23880.16010.97720.48420.09960.19180.20570.1686-0.0065-0.01230.05520.656-17.296-45.286
205.6952-2.32514.27921.77550.846811.36680.99860.1054-0.947-0.0492-0.33850.43342.7831-0.2592-0.66020.6929-0.0266-0.02970.0346-0.02670.2764-4.263-23.008-42.205
215.98220.23762.29764.8742-0.552411.81570.24590.8746-0.5895-0.176-0.1302-0.09661.96990.3974-0.11580.29310.11660.02110.04650.02960.09020.767-18.719-41.599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 114
2X-RAY DIFFRACTION2A115 - 126
3X-RAY DIFFRACTION3A127 - 166
4X-RAY DIFFRACTION4A167 - 229
5X-RAY DIFFRACTION5A230 - 256
6X-RAY DIFFRACTION6A257 - 294
7X-RAY DIFFRACTION7A295 - 323
8X-RAY DIFFRACTION8B70 - 114
9X-RAY DIFFRACTION9B115 - 123
10X-RAY DIFFRACTION10B124 - 161
11X-RAY DIFFRACTION11B162 - 236
12X-RAY DIFFRACTION12B237 - 258
13X-RAY DIFFRACTION13B259 - 290
14X-RAY DIFFRACTION14B291 - 323
15X-RAY DIFFRACTION15C71 - 114
16X-RAY DIFFRACTION16C115 - 141
17X-RAY DIFFRACTION17C142 - 167
18X-RAY DIFFRACTION18C168 - 236
19X-RAY DIFFRACTION19C237 - 250
20X-RAY DIFFRACTION20C251 - 293
21X-RAY DIFFRACTION21C294 - 323

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