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

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Basic information

Entry
Database: PDB / ID: 5ogr
TitleStructure of cathepsin B1 from Schistosoma mansoni in complex with WRR286 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
ACETATE ION / Chem-VS4 / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)87,5649
Polymers85,5223
Non-polymers2,0436
Water15,727873
1
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1883
Polymers28,5071
Non-polymers6812
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)29,1883
Polymers28,5071
Non-polymers6812
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)29,1883
Polymers28,5071
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.484, 78.072, 77.663
Angle α, β, γ (deg.)90.000, 91.240, 90.000
Int Tables number4
Space group name H-MP1211

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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: Pichia (fungus) / Variant (production host): X-33 / References: UniProt: Q8MNY2
#2: Chemical ChemComp-VS4 / 3-[[N-[4-METHYL-PIPERAZINYL]CARBONYL]-PHENYLALANINYL-AMINO]-5-PHENYL-PENTANE-1-SULFONIC ACID BENZYLOXY-AMIDE


Mass: 621.790 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H43N5O5S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 873 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Citrate, 30% PEG 1500 c(protein)= 5 mg/ml ratio protein:reservoir = 1:1ul cryocooled in mother liquor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.55→39.04 Å / Num. obs: 112101 / % possible obs: 98.9 % / Redundancy: 3.313 % / Biso Wilson estimate: 26.825 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.073 / Χ2: 1.112 / Net I/σ(I): 11.81 / Num. measured all: 371394
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.643.310.7071.76179190.6880.84498.1
1.64-1.763.2880.4292.99170520.8690.51399.6
1.76-1.93.4380.2614.97159480.9520.30999.7
1.9-2.083.2440.1428.5146330.9810.1799.4
2.08-2.323.4450.09313.39132350.990.1199.5
2.32-2.683.2350.06517.84116610.9940.07898.9
2.68-3.283.360.04425.8898400.9970.05398.5
3.28-4.633.1330.03232.8675070.9980.03897
4.63-39.043.2080.02635.1943060.9980.03198.1

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Processing

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

4i07


Resolution: 1.55→39.04 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.621 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0743 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.08
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1121 1 %RANDOM
Rwork0.1615 ---
obs0.1619 110979 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.5 Å2 / Biso mean: 27.176 Å2 / Biso min: 11.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å2-0.76 Å2
2--0.15 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.55→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 144 884 7022
Biso mean--20.21 33.68 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196470
X-RAY DIFFRACTIONr_bond_other_d0.0010.025948
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9638759
X-RAY DIFFRACTIONr_angle_other_deg0.872313815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57523.785288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.534151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5211540
X-RAY DIFFRACTIONr_chiral_restr0.1010.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021538
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 80 -
Rwork0.323 8008 -
all-8088 -
obs--96.82 %
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)
14.05742.1243-2.04717.9493-9.849211.52710.09010.29820.18060.041-0.0894-0.6364-0.23490.9509-0.00080.1104-0.00830.01320.2486-0.0230.164132.879-0.58631.658
20.58660.05020.20610.22310.17180.5063-0.01050.00130.0270.0022-0.03770.0276-0.02080.02830.04820.1037-0.0091-0.04760.1195-0.00080.136414.6082.18942.126
333.384322.85532.999215.7092.41823.1542-0.1436-0.33970.4146-0.1626-0.1360.352-0.32180.49350.27960.2025-0.0206-0.10250.24870.0030.362514.03711.49948.479
40.35740.01970.10990.51430.25230.5893-0.00870.00640.0847-0.0175-0.07090.0804-0.0621-0.0780.07960.09780.0163-0.0620.1083-0.01950.16392.047.43537.874
50.906-0.8752-0.34725.19351.09270.8478-0.0324-0.0774-0.09110.1664-0.00570.00760.0669-0.14210.03810.102-0.0248-0.01120.1212-0.010.1661.175-5.14646.497
61.9873-1.67940.06835.5691-1.72541.3343-0.0695-0.116-0.25930.14610.00210.44170.035-0.26290.06740.0721-0.0401-0.00480.1453-0.04840.2064-4.836-7.18242.844
71.7737-0.6249-0.07234.3363-0.80820.1881-0.0137-0.04670.14120.39140.09740.1533-0.0858-0.02-0.08370.1540.0204-0.02650.102-0.0370.1542-114.19651.041
81.3918-0.3811-0.34230.24490.33950.8115-0.00450.08260.1584-0.0716-0.00190.0093-0.09220.19070.00640.1193-0.0188-0.04180.13810.0320.125119.2537.96530.798
90.4250.00590.26510.10240.03230.24140.05710.0443-0.0422-0.0152-0.02610.02930.03760.0573-0.03110.12190.0223-0.05210.1287-0.01510.130914.533-10.99232.594
100.89580.48451.02463.56841.85942.23430.04320.19120.0454-0.2116-0.06240.0054-0.08770.0530.01910.12410.0028-0.02070.14510.02840.096316.2830.73126.905
110.3553-0.12240.37890.33730.3541.37190.02650.0234-0.02030.0921-0.0185-0.05730.11350.0504-0.00790.1269-0.0116-0.05890.11930.01940.110236.0090.36467.491
125.10011.6438-5.12790.5337-1.64485.1882-0.457-0.4592-0.6794-0.1162-0.1746-0.21820.57280.40490.63160.6174-0.0838-0.02270.2750.09980.306532.646-8.03577.4
130.19840.05170.15750.6235-0.21831.45670.13140.0486-0.020.0452-0.04870.03920.2016-0.0846-0.08280.1536-0.0344-0.06060.10980.00830.107326.316-10.07859.65
140.90861.3673-0.48632.0787-0.61262.78330.0739-0.0033-0.26420.0883-0.0245-0.39870.35590.2269-0.04940.18790.0935-0.08040.1268-0.00480.183441.478-15.43959.675
155.7279-0.6318-1.59018.8542-2.02931.55630.110.22220.0050.052-0.1003-0.291-0.07230.3732-0.00960.0531-0.00650.02110.3209-0.03750.152349.024-2.83351.337
166.11524.0105-2.58594.2977-1.93.2316-0.18660.3285-0.3246-0.4590.152-0.24950.68460.17760.03460.23740.0577-0.01430.1285-0.0440.094436.707-13.55747.922
173.1649-0.1658-0.62931.5901-0.67063.04490.1297-0.1461-0.26030.0735-0.058-0.02750.4233-0.0041-0.07180.2416-0.0258-0.10750.04350.04480.110432.92-22.56967.321
180.4252-0.48990.54482.67580.55891.3721-0.1083-0.09960.04580.2532-0.04260.1281-0.0808-0.23280.15090.120.0024-0.02080.1417-0.01220.122324.1366.69869.049
190.1470.06630.2950.45530.0730.6656-0.04150.08110.01470.0431-0.0215-0.0432-0.08650.1030.06310.105-0.0354-0.05630.15030.03310.128338.0099.41457.114
200.96460.9879-0.51732.5648-2.09074.0982-0.0058-0.00010.06390.0574-0.06030.1126-0.0346-0.0410.06620.1156-0.004-0.03390.1336-0.00730.131325.9857.01262.917
212.85550.21181.2670.11350.10930.5711-0.0353-0.32840.2493-0.0754-0.06760.0349-0.0075-0.17630.10290.1244-0.0251-0.0760.1553-0.02920.12582.89838.15363.275
222.67025.27351.728815.69195.03551.6373-1.1424-0.32510.2488-1.68180.78810.9283-0.54360.16360.35430.60560.1798-0.04840.7211-0.030.303-9.54938.27966.785
234.55432.53261.74671.7753-0.1424.12070.135-1.50710.35060.0282-0.70840.04270.2323-0.98010.57340.0547-0.031-0.02390.5862-0.22290.16792.96442.43378.923
246.53992.6758-0.278711.8933-0.69160.1441-0.0272-0.25490.9275-0.4393-0.03850.6161-0.1371-0.17160.06580.29290.2881-0.15720.333-0.22410.3813-4.87154.59669.462
255.89812.6106-2.44121.42980.1979.6855-1.1865-0.45791.1247-0.7225-0.09390.5818-0.85560.17671.28040.45570.101-0.5110.1757-0.31490.933410.07257.28468.629
262.6514-0.1194-1.00111.03891.73183.1621-0.1109-0.00480.53780.0856-0.18370.330.1246-0.28980.29470.13630.10890.10160.4317-0.15940.4533-9.76851.70279.263
271.20310.25881.41560.05640.30541.66870.1023-0.1017-0.06060.0288-0.0212-0.0220.1227-0.1047-0.08110.1375-0.0272-0.08290.10930.00180.125110.78434.65666.866
285.7410.4916-1.1340.09470.55958.5979-0.23810.2539-0.1338-0.03610.07260.0043-0.23160.64050.16540.149-0.0449-0.07310.17030.00810.14227.8443.54866.081
291.92560.35891.42140.46990.52251.2147-0.1380.17760.0370.03750.09010.0532-0.05370.16910.04780.1183-0.0223-0.07070.1354-0.00380.117613.6739.58158.26
306.26821.20290.10420.23770.14272.92350.1125-0.1114-0.16510.036-0.0165-0.04670.3072-0.0891-0.0960.1705-0.0045-0.07730.1037-0.00140.140712.75831.35168.754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 75
2X-RAY DIFFRACTION2A76 - 119
3X-RAY DIFFRACTION3A120 - 124
4X-RAY DIFFRACTION4A125 - 166
5X-RAY DIFFRACTION5A167 - 183
6X-RAY DIFFRACTION6A184 - 199
7X-RAY DIFFRACTION7A200 - 215
8X-RAY DIFFRACTION8A216 - 240
9X-RAY DIFFRACTION9A241 - 307
10X-RAY DIFFRACTION10A308 - 323
11X-RAY DIFFRACTION11B70 - 115
12X-RAY DIFFRACTION12B116 - 123
13X-RAY DIFFRACTION13B124 - 161
14X-RAY DIFFRACTION14B162 - 176
15X-RAY DIFFRACTION15B177 - 187
16X-RAY DIFFRACTION16B188 - 200
17X-RAY DIFFRACTION17B201 - 216
18X-RAY DIFFRACTION18B217 - 237
19X-RAY DIFFRACTION19B238 - 307
20X-RAY DIFFRACTION20B308 - 323
21X-RAY DIFFRACTION21C70 - 117
22X-RAY DIFFRACTION22C118 - 124
23X-RAY DIFFRACTION23C125 - 163
24X-RAY DIFFRACTION24C164 - 171
25X-RAY DIFFRACTION25C172 - 197
26X-RAY DIFFRACTION26C198 - 212
27X-RAY DIFFRACTION27C213 - 259
28X-RAY DIFFRACTION28C260 - 269
29X-RAY DIFFRACTION29C270 - 307
30X-RAY DIFFRACTION30C308 - 323

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