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

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Basic information

Entry
Database: PDB / ID: 6exo
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


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
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-C3E / Cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,17027
Polymers45,8382
Non-polymers2,33125
Water3,945219
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A: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,05413
Polymers22,9191
Non-polymers1,13512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,11614
Polymers22,9191
Non-polymers1,19713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.724, 49.813, 67.466
Angle α, β, γ (deg.)103.860, 98.980, 99.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cysteine protease


Mass: 22919.188 Da / Num. of mol.: 2 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Details: cathepsin L-like cysteine protease with reversible oxidation (sulfenic acid) at its active-site cysteine (Cys25)
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: rhodesain / Plasmid: pPICZAlphaB
Details (production host): AOX1 promoter and extracellular secretion signal
Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q95PM0
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-C3E / (3~{S},14~{E})-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide


Mass: 451.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22ClN3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Description: stable needles, usually micro-needles in rosettes, micro-seeding with crystals of apo protein was applied to grow larger needles
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, crystal 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 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→47.18 Å / Num. obs: 27828 / % possible obs: 91.4 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.058 / Rrim(I) all: 0.091 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4107 / Rpim(I) all: 0.378 / Rrim(I) all: 0.59 / % possible all: 92

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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: 1.9→47.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.078 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.186
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1414 5.1 %RANDOM
Rwork0.1952 ---
obs0.1981 26413 91.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.76 Å2 / Biso mean: 32.919 Å2 / Biso min: 18.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20.84 Å2-0.93 Å2
2--0.28 Å2-0.21 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 1.9→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 156 219 3585
Biso mean--51.05 37.88 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023517
X-RAY DIFFRACTIONr_bond_other_d0.0020.023149
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9564783
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0037261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78226.81163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.655154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 98 -
Rwork0.323 1977 -
all-2075 -
obs--92.39 %
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)
13.8321-1.5953-0.40712.11561.68927.7798-0.1783-0.2119-0.01260.35250.0916-0.2033-0.1754-0.13150.08660.2363-0.0264-0.07240.29640.06380.11510.7436-0.024711.9807
25.9464-3.6254-1.30015.26650.24310.39180.0239-0.47020.01650.4227-0.0692-0.4836-0.12450.17380.04530.2758-0.11530.0050.29810.0630.169812.4762-0.64261.0906
38.37322.8047-1.14963.95330.74571.10430.24530.06390.3551-0.1217-0.19370.0729-0.3078-0.0761-0.05160.15350.0509-0.03050.15070.04370.0921-2.65754.0102-9.507
40.684-0.1769-0.44181.01080.77091.65310.1084-0.0247-0.0901-0.0691-0.1670.0116-0.1026-0.00560.05860.10860.0576-0.03490.19930.06570.0592-2.4201-7.1442-4.9083
511.09253.1228-3.28534.7393-2.31484.23390.261-0.1445-0.17960.2901-0.25440.0485-0.1693-0.0213-0.00670.12840.0614-0.05660.11930.0030.0841-1.752-13.8235-8.6774
63.1191-0.9865-0.53426.59353.50141.8598-0.11310.1903-0.0731-0.51070.08080.0509-0.27090.0480.03230.17080.0953-0.00250.2250.06790.0570.7492-3.5512-16.5808
70.81922.85711.262612.80562.84483.1415-0.23960.13050.0622-0.64790.40520.5657-0.31040.0071-0.16560.2416-0.0301-0.02890.29360.05350.1981-7.276-1.0049-20.1547
823.0164-1.8298-6.87168.11594.24463.76960.21880.65450.3291-0.5942-0.0867-0.0876-0.3118-0.2164-0.13210.27390.0165-0.04580.18860.02240.0939-1.8698-14.0786-18.6809
91.7499-1.5464-0.51453.4941.72072.06310.061-0.128-0.19450.2424-0.18110.09220.2304-0.03790.12010.09710.0035-0.02930.22110.08460.0764-2.9513-10.15093.6414
105.52640.10.9530.76950.59998.4082-0.02-0.06910.1440.07550.0501-0.0571-0.20220.0452-0.03010.11730.0107-0.02210.18010.05790.05181.6838-1.858314.0221
116.2934-3.129-1.404611.7633-1.70795.3227-0.1007-0.5839-0.02750.210.0759-0.15580.35590.05940.02490.14240.0004-0.01610.17180.02810.02343.7399-5.53158.06
121.16980.64170.363710.7402-0.84250.2177-0.021-0.14280.39340.3513-0.11530.0638-0.0474-0.04510.13640.25270.0829-0.01030.24650.06510.1967-6.188510.01563.2054
137.1848-0.54520.11096.0879-1.06220.266-0.0090.25490.6443-0.2328-0.0261-0.0013-0.148-0.02870.03510.47290.0281-0.03710.20810.0160.26151.676317.10541.3906
1411.01699.16766.87097.63775.71254.289-0.0473-0.24090.47070.0136-0.22120.4009-0.0496-0.14270.26850.33940.0278-0.00620.28410.01290.2566-5.710216.14878.7989
151.51911.5401-1.29992.5113-0.22652.38180.12150.03160.1984-0.0349-0.03750.2469-0.3133-0.0577-0.0840.21530.0454-0.06990.25310.08970.1058-2.23944.96244.1043
1614.294-1.5168-1.96566.94310.69069.56620.1186-0.5960.72450.2151-0.0166-0.335-0.49250.4624-0.1020.2131-0.0271-0.0720.224-0.00620.19618.892511.357615.2921
170.48080.16811.28860.9041.32274.3605-0.05180.09120.166-0.1824-0.0938-0.2338-0.33510.14480.14560.2552-0.0255-0.01330.26920.09350.22844.68879.53-1.5404
187.5246-1.97630.42556.2095-2.97533.32140.0372-0.52440.29570.2835-0.01660.0465-0.52640.0031-0.02060.2156-0.0351-0.03550.18730.03530.13564.66511.12076.1854
192.4291-0.3231-0.18651.0371.89473.5370.0625-0.45480.0796-0.1458-0.0432-0.0234-0.3024-0.1779-0.01930.33080.031-0.04310.2930.03680.1664-4.01748.784112.4028
204.1281-2.8272-4.277410.46865.94385.9917-0.0992-0.054-0.00280.28880.04910.05680.0549-0.12610.05010.1161-0.01-0.03080.19830.05320.0575-3.7721-6.68356.1611
211.41960.7973-0.434810.35461.59655.7284-0.14940.27790.2076-0.28930.1496-0.0422-0.4545-0.0813-0.00020.1120.0423-0.03570.24810.01270.194-1.193127.6122-32.2052
223.18662.17892.05331.58070.552212.2485-0.04630.15760.43530.00180.12830.3617-0.3234-0.767-0.0820.0610.0121-0.00630.27760.02690.1591-2.198116.0198-26.5963
2312.42461.8014-3.91694.37732.25158.87030.2832-0.6616-0.0660.7633-0.1022-0.3920.09590.2803-0.1810.19360.0527-0.06250.18820.06290.09812.42368.5505-16.9186
243.62151.21230.44591.25830.53650.28210.01720.17850.0568-0.0338-0.02830.00690.0143-0.12610.01110.1265-0.0112-0.02290.28670.02030.07157.004411.4125-31.133
253.12460.23360.99770.0274-0.1578.36480.0015-0.08310.0046-0.01680.03660.02110.1431-0.7406-0.03810.1956-0.0072-0.0880.30580.05160.1858-1.18499.4458-35.0862
265.74121.5774-1.41473.01960.43170.9453-0.0033-0.0473-0.07260.1303-0.0143-0.22920.35580.07060.01760.35420.0878-0.02060.25450.06260.144816.693.463-27.3859
272.62340.9154-0.85621.95140.91931.1903-0.18510.1105-0.0505-0.07080.3947-0.33130.06040.2495-0.20960.20430.0707-0.05950.30270.02660.165717.83499.1662-31.8729
288.58161.984-3.81213.6618-0.73575.293-0.10850.1096-0.34490.01650.0434-0.08040.3468-0.23220.06510.17850.0132-0.0770.15840.02890.06539.62821.5706-34.8557
293.4125-1.69661.33261.0842-1.90717.044-0.1244-0.2076-0.5234-0.03620.1220.20360.6081-0.1710.00240.29770.0236-0.09760.21960.08110.194410.9773-0.4492-19.5926
303.25710.6190.16335.62465.44345.3278-0.59090.6188-0.3361-0.08340.39970.1423-0.00410.3150.19120.41920.0217-0.05880.32530.04690.255312.8566-7.4276-28.6745
311.3551-0.4655-0.29372.26590.64142.86590.03120.20910.0195-0.3327-0.017-0.0965-0.1691-0.173-0.01420.15740.0374-0.01840.2770.0740.04669.988217.6533-36.1586
323.84481.67333.87272.35932.66319.0762-0.00320.09390.1142-0.01860.0787-0.0391-0.16250.071-0.07550.08880.036-0.02420.10350.05470.072211.284722.1869-26.3835
3311.0632-1.23963.37268.1255-0.536813.68520.0161-1.0015-0.07120.71790.2407-0.4505-0.14730.5853-0.25680.1835-0.0013-0.04680.2213-0.00260.13879.349622.8359-11.3345
347.6775-0.4315-1.88210.03260.10770.468-0.1503-0.1453-0.21220.01080.06180.01630.01470.04030.08840.20980.0506-0.04030.29140.00340.200210.925830.8481-15.3636
358.46181.01243.14763.00461.0974.7805-0.1595-0.0923-0.03690.18990.1759-0.218-0.16690.2613-0.01640.10560.0351-0.03140.13850.03880.065314.324520.8442-22.7291
360.9602-1.64252.107614.0753-8.64886.895-0.1389-0.01250.2617-0.3925-0.19170.0819-0.07380.07530.33060.35390.06830.03630.23740.03640.2241.009432.9919-27.0733
370.240.9918-0.43265.8912-0.77381.9321-0.0093-0.00130.07330.06030.11310.03-0.1049-0.0334-0.10380.08090.0939-0.05340.20260.02270.15095.319124.6884-20.911
383.6659-0.28230.34418.4235-1.57295.92880.03770.0044-0.12910.24550.14580.348-0.1182-0.3902-0.18350.08960.0955-0.01850.1610.01690.05823.185822.0069-16.5457
395.0815-5.12323.10686.7487-1.20184.2622-0.03730.00170.4762-0.1542-0.0038-0.6963-0.2885-0.04340.04110.19320.048-0.03520.24420.02050.143313.748330.8475-23.7439
404.0968-1.6364-1.17992.1944-1.16692.08260.19980.02050.3948-0.2081-0.1281-0.20370.08030.1292-0.07170.1380.0607-0.00080.31520.07420.108513.043319.5323-34.9567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 15
3X-RAY DIFFRACTION3A16 - 26
4X-RAY DIFFRACTION4A27 - 76
5X-RAY DIFFRACTION5A77 - 86
6X-RAY DIFFRACTION6A87 - 94
7X-RAY DIFFRACTION7A95 - 101
8X-RAY DIFFRACTION8A102 - 106
9X-RAY DIFFRACTION9A107 - 121
10X-RAY DIFFRACTION10A122 - 130
11X-RAY DIFFRACTION11A131 - 136
12X-RAY DIFFRACTION12A137 - 143
13X-RAY DIFFRACTION13A144 - 151
14X-RAY DIFFRACTION14A152 - 158
15X-RAY DIFFRACTION15A159 - 169
16X-RAY DIFFRACTION16A170 - 177
17X-RAY DIFFRACTION17A178 - 192
18X-RAY DIFFRACTION18A193 - 197
19X-RAY DIFFRACTION19A198 - 206
20X-RAY DIFFRACTION20A207 - 215
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 17
23X-RAY DIFFRACTION23B18 - 25
24X-RAY DIFFRACTION24B26 - 39
25X-RAY DIFFRACTION25B40 - 48
26X-RAY DIFFRACTION26B49 - 62
27X-RAY DIFFRACTION27B63 - 76
28X-RAY DIFFRACTION28B77 - 87
29X-RAY DIFFRACTION29B88 - 98
30X-RAY DIFFRACTION30B99 - 105
31X-RAY DIFFRACTION31B106 - 130
32X-RAY DIFFRACTION32B131 - 143
33X-RAY DIFFRACTION33B144 - 148
34X-RAY DIFFRACTION34B149 - 157
35X-RAY DIFFRACTION35B158 - 167
36X-RAY DIFFRACTION36B168 - 173
37X-RAY DIFFRACTION37B174 - 185
38X-RAY DIFFRACTION38B186 - 197
39X-RAY DIFFRACTION39B198 - 205
40X-RAY DIFFRACTION40B206 - 215

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