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

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Basic information

Entry
Database: PDB / ID: 6exq
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 ...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-C2W / Cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,0859
Polymers45,8062
Non-polymers1,2787
Water1,874104
1
A: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5114
Polymers22,9031
Non-polymers6083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5735
Polymers22,9031
Non-polymers6704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.336, 50.176, 60.570
Angle α, β, γ (deg.)105.280, 96.920, 99.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cysteine protease /


Mass: 22903.188 Da / Num. of mol.: 2 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Details: cathepsin L-like cysteine protease
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-C2W / (3~{S})-19-chloranyl-~{N}-(1-cyanocyclopropyl)-8-methoxy-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(20),6(11),7,9,18,21-hexaene-3-carboxamide


Mass: 483.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26ClN3O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.95 Å3/Da / Density % sol: 36.99 %
Description: small, stable needles; despite micro-seeding only very few crystals reached sufficient size
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 PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 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: 2.5→47.45 Å / Num. obs: 11526 / % possible obs: 96.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.085 / Rrim(I) all: 0.162 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1722 / Rpim(I) all: 0.538 / Rrim(I) all: 1.048 / % possible all: 96.6

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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: 2.5→47.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.923 / SU B: 33.572 / SU ML: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 550 4.8 %RANDOM
Rwork0.1704 ---
obs0.1745 10975 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.42 Å2 / Biso mean: 48.73 Å2 / Biso min: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å2-0.27 Å20.5 Å2
2---0.43 Å2-2.3 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 2.5→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 88 104 3400
Biso mean--72.15 41.83 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023411
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9464660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3485440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41226.709158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34515486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.985154
X-RAY DIFFRACTIONr_chiral_restr0.0950.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212682
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 40 -
Rwork0.291 815 -
all-855 -
obs--96.83 %
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)
18.50393.26042.67291.26471.03670.86440.28150.1858-0.830.17970.0397-0.34080.1830.0924-0.32120.65630.0513-0.05010.3211-0.09150.40899.5928-12.2904-5.1372
20.12880.82570.43755.43032.42593.61550.09790.044-0.03030.45280.2967-0.11530.01270.5043-0.39460.22550.0134-0.05870.3178-0.13990.11183.82343.38233.6341
33.8063-2.2093-3.9292.38774.54519.6294-0.27440.6637-0.4787-0.28750.01190.1382-0.23550.37310.26250.3692-0.10990.09370.4705-0.17160.30023.00644.1657-5.1487
42.3397-2.308-3.9396.63858.113410.7547-0.1957-0.180.1047-0.84620.4396-0.0746-0.72340.6568-0.24390.4366-0.10860.09510.4911-0.13410.256210.14945.9505-7.7995
513.3314-7.0089-0.91817.65469.110418.8968-0.16680.1064-0.46420.20080.34360.12940.36190.7448-0.17670.2288-0.1040.05870.23540.01260.2317-2.375913.10590.17
611.49585.19433.373915.411112.589810.3776-0.29870.3719-0.07570.14490.11210.20810.08510.1040.18650.3192-0.0989-0.02230.23680.06520.1903-10.531213.4547-2.871
78.04874.76140.240310.23620.92152.2854-0.36080.56150.11750.32050.46340.6710.377-0.3005-0.10260.136-0.0194-0.01550.2406-0.00360.2091-10.70376.6201-0.6299
81.2412-2.65670.3457.1527-4.715810.9420.2670.299-0.2096-0.4945-0.52460.3623-0.1828-0.08970.25760.3332-0.1501-0.1030.39030.00790.3235-6.610711.0013-10.7629
97.54722.8342-4.90744.3073-2.05373.2095-0.109-0.53740.1438-0.25210.1376-0.2140.08930.3607-0.02860.4219-0.08390.00640.4989-0.03760.31042.779815.6168-0.1677
109.67170.70962.67240.3046-0.33511.8642-0.26190.29060.4211-0.17980.26560.07170.2085-0.4113-0.00370.6404-0.03070.04760.2647-0.00620.4319-4.411421.11732.7431
117.44362.5797-6.86772.8171-5.336711.03070.30670.15650.4033-0.2016-0.3179-0.0718-0.08850.60270.01130.6131-0.1827-0.09050.4533-0.03140.26533.517513.7917-10.3619
120.0613-0.94550.579332.7896-10.83765.7904-0.05180.00420.00260.2480.0924-0.0158-0.3254-0.133-0.04070.2066-0.0742-0.02890.36360.02960.2422-6.5257-1.7354-12.0631
137.0226-3.2412-0.58128.46210.200410.7547-0.06220.0990.0301-0.2871-0.13560.09290.50190.23220.19770.2159-0.01190.04210.2233-0.15290.1297-1.0345-12.7013-8.3041
148.3846-0.5562-3.31013.85721.35011.69650.21610.2596-0.44050.2994-0.1578-0.3624-0.1669-0.1613-0.05830.55880.05580.10830.2275-0.01710.3589-3.1434-5.35595.7421
158.6947-7.73835.09696.9068-4.4964.6848-0.0585-0.4172-0.04650.12890.37530.06930.0314-0.2228-0.31680.3250.01570.01010.2848-0.04660.2581-4.8304-9.85810.8024
166.203-2.4508-3.234813.59018.045.3122-0.0760.1947-0.24850.3670.2976-0.53130.20370.1278-0.22170.1856-0.0592-0.05610.2962-0.12710.14723.4937-8.37810.0253
178.50610.8504-11.45172.0634-3.253217.6658-0.6808-0.2593-0.7682-0.16260.20620.44990.98430.09170.47460.43770.033-0.09430.2805-0.0520.33856.0787-20.08694.2954
180.28640.0472-0.92413.2835-0.08793.00540.0067-0.19410.07450.40080.3141-0.20990.00820.7036-0.32080.31020.1217-0.08180.434-0.29490.2894.8231-3.92688.8111
197.81061.4324-1.25191.30723.361612.7641-0.17580.2771-0.63630.19480.0584-0.13210.5364-0.02640.11740.39690.0569-0.04850.1348-0.05320.3204-5.5347-13.59452.8042
204.28722.8131-5.67137.2721-12.235620.9208-0.16650.46580.1359-0.51120.27660.03460.7663-0.4433-0.11010.4428-0.14120.04590.3658-0.09090.2188-1.7118-0.3537-11.137
211.38173.0349-1.10066.7048-2.41020.8876-0.01740.0460.11260.01220.07110.39990.0129-0.1222-0.05370.32590.02160.12440.7042-0.1660.6365-2.35615.253635.8783
2213.0943-1.7587-1.48621.9680.87516.4870.04760.13560.3371-0.6173-0.25510.3521-0.1976-0.21950.20750.27260.0398-0.06040.2175-0.14880.29637.164412.24917.7486
230.71251.1448-1.64752.1293-1.53018.1538-0.0413-0.1045-0.1201-0.0964-0.2466-0.17830.1191-0.06570.28790.11830.0287-0.04920.2304-0.15880.239110.818318.850322.7965
242.914-1.4337-5.81942.59543.291811.9417-0.10060.0202-0.0317-0.006-0.22680.304-0.0799-0.2260.32740.33370.1044-0.18730.2098-0.25350.32112.909825.239423.4814
254.42680.7814-0.55426.5655-1.67395.62260.0241-0.27250.1479-0.1304-0.359-0.4961-0.59470.31890.33490.12440.0358-0.02330.1654-0.05350.198819.649421.785120.3252
265.2379-0.55990.87180.45331.711212.39690.1177-0.25030.3778-0.1946-0.17330.0409-0.1828-0.24230.05560.28640.1655-0.12790.237-0.13860.217712.447629.993919.5056
272.01950.73390.17280.2861-0.01080.58420.06170.3229-0.1485-0.05260.0209-0.04740.49690.0468-0.08260.62440.1702-0.08840.4701-0.1490.38611.35118.39958.876
2814.9696-4.7213-4.87917.5901-5.47969.70310.41820.9133-0.753-0.6244-0.30430.61310.3657-0.2114-0.1140.4866-0.0439-0.04330.3746-0.06290.369714.344828.95497.3227
292.13832.3384-0.82712.5598-0.90490.32190.1456-0.09230.40910.0934-0.06130.4473-0.05370.0223-0.08420.29980.1176-0.15520.2686-0.21370.31129.344330.361522.7654
308.05610.87740.813412.30321.39743.45050.193-0.29060.4070.4878-0.16610.3132-0.10680.1595-0.02690.2022-0.0715-0.03440.3066-0.11740.095912.814116.834541.1733
3124.7818-7.6742-7.69926.4467-1.44933.0048-0.0715-0.6169-0.22761.0148-0.0834-0.2843-0.12880.23040.15490.26410.04190.00230.4175-0.06880.33664.00620.283537.6075
326.3032-7.4503-4.68469.20315.33883.61020.4575-0.06210.0168-0.9548-0.23010.2308-0.16780.1066-0.22740.44310.1331-0.18320.377-0.12530.354214.78828.504229.7339
3315.34532.0185-2.831724.07296.663313.3831-0.08720.0965-0.8703-0.385-0.4033-0.39781.27830.21860.49050.2387-0.0212-0.01360.2070.04150.21649.2071-1.374725.5441
347.73153.4929-8.20121.5843-3.71718.74780.2884-0.71840.0730.0914-0.29460.0268-0.18710.73870.00620.4043-0.08920.04570.2509-0.01930.343211.0003-1.551934.1847
3510.73315.4661-7.21612.70914.96312.3708-0.314-0.1473-1.17070.27640.0099-1.14290.60580.19440.30410.42010.0302-0.04990.3081-0.05560.366820.73995.933229.1164
360.0710.53560.27284.20452.12661.07690.0165-0.02850.03380.1558-0.07660.08850.0733-0.04660.06010.2766-0.11840.0730.4787-0.11180.25536.374712.674232.5166
374.755710.0831-4.83621.9306-9.60816.4846-0.25390.2838-0.1241-0.22320.3044-0.35710.1448-0.4628-0.05050.5032-0.207-0.01650.4359-0.04770.24681.55992.970142.4809
381.162-0.3669-3.69840.86331.363511.8550.01020.1216-0.0687-0.0521-0.32870.35380.0191-0.53990.31840.1929-0.0342-0.03280.3305-0.17320.2944.68246.243725.9936
3913.0472-2.81632.33850.94230.27852.5427-0.0322-0.3523-0.39050.27240.00060.20710.55230.12480.03160.3411-0.15510.06380.4061-0.13020.354211.4844.046837.5378
402.60691.1228-0.21490.68120.93685.4062-0.2071-0.28090.0091-0.0919-0.10190.05230.02070.01840.3090.2102-0.0459-0.0380.3087-0.15470.134113.696319.673934.0239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 27
3X-RAY DIFFRACTION3A28 - 38
4X-RAY DIFFRACTION4A39 - 49
5X-RAY DIFFRACTION5A50 - 54
6X-RAY DIFFRACTION6A55 - 60
7X-RAY DIFFRACTION7A61 - 71
8X-RAY DIFFRACTION8A72 - 81
9X-RAY DIFFRACTION9A82 - 94
10X-RAY DIFFRACTION10A95 - 105
11X-RAY DIFFRACTION11A106 - 113
12X-RAY DIFFRACTION12A114 - 118
13X-RAY DIFFRACTION13A119 - 131
14X-RAY DIFFRACTION14A132 - 146
15X-RAY DIFFRACTION15A147 - 162
16X-RAY DIFFRACTION16A163 - 170
17X-RAY DIFFRACTION17A171 - 177
18X-RAY DIFFRACTION18A178 - 195
19X-RAY DIFFRACTION19A196 - 208
20X-RAY DIFFRACTION20A209 - 215
21X-RAY DIFFRACTION21B1 - 12
22X-RAY DIFFRACTION22B13 - 23
23X-RAY DIFFRACTION23B24 - 35
24X-RAY DIFFRACTION24B36 - 52
25X-RAY DIFFRACTION25B53 - 73
26X-RAY DIFFRACTION26B74 - 86
27X-RAY DIFFRACTION27B87 - 99
28X-RAY DIFFRACTION28B100 - 104
29X-RAY DIFFRACTION29B105 - 116
30X-RAY DIFFRACTION30B117 - 128
31X-RAY DIFFRACTION31B129 - 134
32X-RAY DIFFRACTION32B135 - 143
33X-RAY DIFFRACTION33B144 - 149
34X-RAY DIFFRACTION34B150 - 156
35X-RAY DIFFRACTION35B157 - 162
36X-RAY DIFFRACTION36B163 - 169
37X-RAY DIFFRACTION37B170 - 176
38X-RAY DIFFRACTION38B177 - 194
39X-RAY DIFFRACTION39B195 - 204
40X-RAY DIFFRACTION40B205 - 215

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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