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- PDB-6ex8: Crystal Structure of Rhodesain in complex with a Macrolactam Inhibitor -

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Basic information

Entry
Database: PDB / ID: 6ex8
TitleCrystal Structure of Rhodesain in complex with a Macrolactam Inhibitor
ComponentsCysteine protease
KeywordsHYDROLASE / Cysteine Protease / Papain-like Protease / Cathepsin L-like Protease / Endopeptidase
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis
Similarity search - Function
Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-C2K / Cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDietzel, U. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: J. Med. Chem. / Year: 2018
Title: Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and Trypanosoma brucei Inhibitors.
Authors: Giroud, M. / Dietzel, U. / Anselm, L. / Banner, D. / Kuglstatter, A. / Benz, J. / Blanc, J.B. / Gaufreteau, D. / Liu, H. / Lin, X. / Stich, A. / Kuhn, B. / Schuler, F. / Kaiser, M. / Brun, R. ...Authors: Giroud, M. / Dietzel, U. / Anselm, L. / Banner, D. / Kuglstatter, A. / Benz, J. / Blanc, J.B. / Gaufreteau, D. / Liu, H. / Lin, X. / Stich, A. / Kuhn, B. / Schuler, F. / Kaiser, M. / Brun, R. / Schirmeister, T. / Kisker, C. / Diederich, F. / Haap, W.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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
Revision 2.0Feb 26, 2025Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease
B: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,24621
Polymers46,1472
Non-polymers2,09919
Water6,503361
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A: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9688
Polymers23,0731
Non-polymers8947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,27813
Polymers23,0731
Non-polymers1,20512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.830, 49.753, 67.569
Angle α, β, γ (deg.)103.560, 98.890, 100.810
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cysteine protease


Mass: 23073.354 Da / Num. of mol.: 2 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Details: causes the acute form of sleeping sickness
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: rhodesain / Plasmid: pPICzAlphaB
Details (production host): AOX1 promoter and signal for extracellular secretion
Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q95PM0
#2: Chemical ChemComp-C2K / (3~{S})-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-9-(trifluoromethyl)-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,18(22),19-hexaene-3-carboxamide


Mass: 521.916 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23ClF3N3O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Description: stable needles, usually micro-needles in rosettes; their size was enhanced using micro-seeding with crystals of apo protein
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.3 - 1.7 M ammonium sulfate 100 mM sodium citrate pH 5.0 growth in 4-8 weeks

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2013
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→47.03 Å / Num. obs: 48169 / % possible obs: 94.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6959 / Rpim(I) all: 0.496 / Rrim(I) all: 0.96 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.22data extraction
XDS2013data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P7U

2p7u


Resolution: 1.6→47.03 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 4.312 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.084
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 2443 5.1 %RANDOM
Rwork0.1363 ---
obs0.1384 45725 94.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.63 Å2 / Biso mean: 25.444 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å21.03 Å2-0.75 Å2
2--0.6 Å2-0.23 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 1.6→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 140 361 3735
Biso mean--43.26 36.23 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023486
X-RAY DIFFRACTIONr_bond_other_d0.0030.023093
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9594743
X-RAY DIFFRACTIONr_angle_other_deg1.4573.0057134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.92526.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0115485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.337154
X-RAY DIFFRACTIONr_chiral_restr0.120.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 174 -
Rwork0.298 3318 -
all-3492 -
obs--93.22 %
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)
11.66510.24530.83441.07932.76237.1332-0.0902-0.13080.0493-0.00260.00380.0212-0.10660.05940.08640.2514-0.0804-0.06060.20440.02310.192910.60920.644410.8176
211.2681-5.09436.17014.882-3.856.161-0.0561-0.11740.3445-0.0518-0.1211-0.3112-0.1260.09690.17720.0761-0.03830.02150.0591-0.00190.08266.4972.1404-4.5751
32.1335-0.63290.29251.8841-0.2061.80550.00580.0113-0.113-0.0191-0.0662-0.0616-0.00880.12460.06040.0512-0.01040.00490.06780.01450.07052.872-6.0824-2.8973
41.8567-0.5581-0.16082.8528-0.29933.093-0.05040.1368-0.0411-0.084-0.05310.0858-0.0238-0.16030.10360.05880.0105-0.02370.0659-0.02790.0599-9.4103-4.8042-10.4646
52.621-1.8576-0.76616.09231.36132.6775-0.0192-0.0642-0.23480.0128-0.06710.27030.1252-0.17210.08630.0407-0.0235-0.00040.0703-0.01850.0792-8.2747-11.194-3.3535
69.54973.6469-6.02845.0728-4.617812.45380.17330.16340.1473-0.1273-0.1570.12-0.06210.1859-0.01630.0560.03040.01140.059-0.01070.05823.4187-9.9061-12.2098
72.6579-3.31130.57748.50921.71581.4990.02870.1920.164-0.4671-0.1589-0.0125-0.19530.04870.13010.1599-0.0156-0.01280.15120.03590.118-1.6995-0.0097-17.2391
81.2312-3.57161.20421.82960.22942.69040.02850.15320.0943-0.4746-0.0811-0.35370.07460.13250.05260.1538-0.0241-0.00210.172-0.00450.1554-7.7221-5.0037-19.9529
91.7254-0.2499-1.00291.66390.20695.36240.0495-0.0073-0.154-0.138-0.0523-0.00190.2547-0.01710.00280.0789-0.01190.01690.0315-0.01460.1014-0.9222-14.4415-6.5541
103.7702-2.2451-4.193811.61685.23617.9475-0.091-0.33180.01690.36520.02490.11620.0701-0.16960.06610.1286-0.01020.01420.17060.01430.0848-7.16-2.840313.6613
112.3758-0.04710.01225.51091.2163.20690.0158-0.43910.07820.2941-0.00090.0061-0.30470.01-0.01490.16150.0011-0.01060.1035-0.01110.0211-0.38460.222716.4117
1212.26353.9212-4.672916.05717.02038.6965-0.163-0.4334-0.21390.36240.0979-0.31670.43150.30890.06510.0973-0.0007-0.00850.10230.02610.05694.185-6.612.0259
132.9327-2.12171.04263.807-1.09721.6245-0.0082-0.1330.16540.1957-0.00910.0454-0.2569-0.16170.01730.1160.00490.00480.0863-0.00530.0746-3.79535.61744.3893
1419.0207-1.35997.683713.15180.728817.1029-0.26811.00571.1398-0.4143-0.13820.1179-1.21120.13390.40630.22760.0020.02050.10750.00070.1796-0.220717.2791-0.0378
158.56460.0712-2.44990.0055-0.01620.70940.08230.32640.5582-0.01480.03550.0219-0.0682-0.0913-0.11780.39520.0045-0.03170.1951-0.01440.32-0.487917.08948.7241
166.71442.10160.459711.06665.387517.53110.12570.08110.62830.0325-0.44050.6362-0.7273-0.85860.31480.10630.05460.02310.1333-0.00730.1593-12.611910.77245.2176
176.20.07873.83990.0101-0.07634.535-0.14440.04870.13210.02340.0006-0.0052-0.2394-0.0310.14380.1587-0.0276-0.03270.08150.00980.1331.47183.49715.1246
1812.7652-1.6463-1.81817.83130.92925.92830.0026-0.86940.36190.6910.0031-0.5688-0.58920.561-0.00570.2014-0.0671-0.08050.1555-0.05030.12328.452711.314215.8132
191.317-0.5668-0.00911.4162-0.38835.64140.0408-0.00680.24180.1065-0.0746-0.1627-0.46030.06350.03370.1149-0.0449-0.02810.02330.00830.10644.08539.93652.0944
201.415-1.5697-0.65995.99571.94352.767-0.0468-0.150.0660.2386-0.0068-0.0016-0.1447-0.14090.05360.0778-0.00220.01170.0747-0.01240.0391-5.28030.97629.2091
211.5853-0.74961.60210.16281.32182.5041-0.16290.09740.1257-0.13450.06510.0865-0.418-0.17690.09780.19370.0861-0.00530.24260.01090.1862-2.370225.9211-30.6466
225.46831.09343.12283.7511-4.352314.1277-0.27750.20180.42980.08450.15270.3315-0.6152-0.90370.12480.07040.02310.00160.1673-0.01390.1272-3.429115.7851-27.2678
235.38890.4978-2.42242.74910.64517.1036-0.0059-0.2571-0.18110.1885-0.0534-0.07230.10230.19220.05930.07340.0254-0.01930.0550.00260.044611.34288.7453-19.6143
242.60780.79171.65362.52410.56714.20120.00010.23320.146-0.09240.02290.08770.0042-0.1981-0.02290.0435-0.00580.00190.10350.00290.04473.428412.0991-34.1648
252.0345-0.36570.84541.5992-0.70032.0421-0.0082-0.0589-0.16130.00370.0565-0.05080.168-0.0687-0.04840.07870.01020.00550.0568-0.02220.031110.99064.5524-28.8622
262.2311-0.00250.37262.65351.36483.5907-0.07210.125-0.0397-0.09190.1017-0.17610.01460.2199-0.02960.06090.02710.00850.0756-0.01430.043517.15227.805-33.0746
278.47512.5126-7.90362.2761-4.75712.27180.0138-0.1111-0.04940.04870.12320.11940.0978-0.0815-0.1370.0972-0.0098-0.01070.0806-0.01490.07545.53750.4858-31.8731
282.1663-0.061.8381.33781.67796.3347-0.0306-0.1543-0.28820.1480.15750.04890.5067-0.1068-0.1270.13980.0209-0.00910.05350.01450.059112.4104-1.5897-20.2402
2914.1705-5.86055.015412.151-7.70038.98820.112-0.1047-0.7971-0.06240.02520.18760.42440.1608-0.13720.1656-0.01360.00490.0934-0.05480.11917.6591-6.0229-32.133
303.64054.9334-0.21046.889-0.95492.5022-0.11690.10420.0942-0.16640.10980.1323-0.0528-0.01560.00720.06290.0150.01560.0770.00090.06110.81611.3487-39.7465
316.9854-1.8011-0.61022.69231.10153.71810.0950.08450.3638-0.273-0.092-0.1171-0.50690.1931-0.00310.189-0.01940.02220.04680.01910.027712.264828.7216-34.0772
329.95561.9635-1.332212.47384.651811.3125-0.05470.62770.0346-0.70140.12040.322-0.2155-0.4193-0.06570.16470.0795-0.01750.1715-0.00670.04913.920924.0899-37.5782
330.27410.1072-0.32091.1740.31830.55490.1046-0.00640.0587-0.0112-0.09460.107-0.162-0.0336-0.010.19760.0083-0.02460.1482-0.0380.16711.740421.6057-22.3174
3434.2932-17.07998.998718.5281-7.142212.6301-0.2247-1.2843-0.33660.87030.3422-0.25310.01640.0841-0.11750.1763-0.02220.00440.1302-0.02830.12747.368623.3365-9.9462
356.16670.179-2.64932.9516-0.35091.1672-0.1136-0.37430.12990.17860.1593-0.02820.00380.1423-0.04570.26320.027-0.02010.137-0.06860.08329.682630.6946-15.1585
363.30634.4829-0.391419.06723.59821.55290.1672-0.4808-0.1790.65780.0822-0.90030.03190.3729-0.24940.1617-0.0271-0.020.21090.00050.142119.134421.9609-19.3552
370.4342-0.51320.19912.9556-0.42190.68540.0217-0.0434-0.00750.07890.00020.0941-0.2251-0.2057-0.0220.11030.05220.00680.0978-0.0210.0642.997523.4165-20.494
386.35022.1372-6.58767.7037-6.888810.45910.2527-0.06260.30550.2582-0.2122-0.1128-0.64110.1344-0.04050.19580.0259-0.01720.0938-0.02250.10636.134431.2716-21.5603
391.7536-0.41362.76051.50381.24856.9454-0.05370.01190.1793-0.07560.1288-0.3003-0.29630.2035-0.07510.2394-0.030.02260.1029-0.04370.169914.523929.6458-23.6368
405.03845.43412.78049.7975.09236.0940.11090.1357-0.03740.070.1196-0.2214-0.09760.0781-0.23040.0781-0.00030.01570.0705-0.00240.062212.782718.9342-34.6688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 21
3X-RAY DIFFRACTION3A22 - 49
4X-RAY DIFFRACTION4A50 - 65
5X-RAY DIFFRACTION5A66 - 82
6X-RAY DIFFRACTION6A83 - 88
7X-RAY DIFFRACTION7A89 - 96
8X-RAY DIFFRACTION8A97 - 102
9X-RAY DIFFRACTION9A103 - 116
10X-RAY DIFFRACTION10A117 - 121
11X-RAY DIFFRACTION11A122 - 127
12X-RAY DIFFRACTION12A128 - 132
13X-RAY DIFFRACTION13A133 - 143
14X-RAY DIFFRACTION14A144 - 148
15X-RAY DIFFRACTION15A149 - 156
16X-RAY DIFFRACTION16A157 - 161
17X-RAY DIFFRACTION17A162 - 169
18X-RAY DIFFRACTION18A170 - 177
19X-RAY DIFFRACTION19A178 - 199
20X-RAY DIFFRACTION20A200 - 215
21X-RAY DIFFRACTION21B1 - 8
22X-RAY DIFFRACTION22B9 - 16
23X-RAY DIFFRACTION23B17 - 28
24X-RAY DIFFRACTION24B29 - 42
25X-RAY DIFFRACTION25B43 - 62
26X-RAY DIFFRACTION26B63 - 80
27X-RAY DIFFRACTION27B81 - 88
28X-RAY DIFFRACTION28B89 - 101
29X-RAY DIFFRACTION29B102 - 108
30X-RAY DIFFRACTION30B109 - 116
31X-RAY DIFFRACTION31B117 - 127
32X-RAY DIFFRACTION32B128 - 132
33X-RAY DIFFRACTION33B133 - 144
34X-RAY DIFFRACTION34B145 - 149
35X-RAY DIFFRACTION35B150 - 156
36X-RAY DIFFRACTION36B157 - 163
37X-RAY DIFFRACTION37B164 - 194
38X-RAY DIFFRACTION38B195 - 199
39X-RAY DIFFRACTION39B200 - 206
40X-RAY DIFFRACTION40B207 - 215

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