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- PDB-4klb: Crystal Structure of Cruzain in complex with the non-covalent inh... -

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Basic information

Entry
Database: PDB / ID: 4klb
TitleCrystal Structure of Cruzain in complex with the non-covalent inhibitor Nequimed176
ComponentsCruzipain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Protease / Thiol protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cruzipain / 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 ...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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-1RV / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsFernandes, W.B. / Montanari, C.A. / Mckerrow, J.H.
CitationJournal: Plos Negl Trop Dis / Year: 2013
Title: Non-peptidic Cruzain Inhibitors with Trypanocidal Activity Discovered by Virtual Screening and In Vitro Assay.
Authors: Wiggers, H.J. / Rocha, J.R. / Fernandes, W.B. / Sesti-Costa, R. / Carneiro, Z.A. / Cheleski, J. / da Silva, A.B. / Juliano, L. / Cezari, M.H. / Silva, J.S. / McKerrow, J.H. / Montanari, C.A.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cruzipain
B: Cruzipain
C: Cruzipain
D: Cruzipain
E: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4268
Polymers113,5765
Non-polymers8503
Water1,964109
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9982
Polymers22,7151
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9982
Polymers22,7151
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9982
Polymers22,7151
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7151
Polymers22,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7151
Polymers22,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.720, 138.720, 163.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 5 / Fragment: CRUZAIN MATURE DOMAIN, UNP residues 123-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Cruzipain, GenBank M84342.1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P25779, cruzipain
#2: Chemical ChemComp-1RV / 2-{[(1H-1,2,4-triazol-5-ylsulfanyl)acetyl]amino}thiophene-3-carboxamide


Mass: 283.330 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H9N5O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Bicine pH 9.0, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.62→39.23 Å / Num. all: 48550 / Num. obs: 48282 / % possible obs: 99.5 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.037
Reflection shellResolution: 2.62→2.71 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.1 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KKU
Resolution: 2.62→39.226 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7997 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1954 4.05 %RAMDOM
Rwork0.1899 ---
all0.1919 48550 --
obs0.1919 48258 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.79 Å2 / Biso mean: 33.8321 Å2 / Biso min: 2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.62→39.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7960 0 54 109 8123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088227
X-RAY DIFFRACTIONf_angle_d1.07611235
X-RAY DIFFRACTIONf_chiral_restr0.0471235
X-RAY DIFFRACTIONf_plane_restr0.0061462
X-RAY DIFFRACTIONf_dihedral_angle_d13.8852750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.62-2.68550.37811310.29793197332898
2.6855-2.75810.33051340.26763201333598
2.7581-2.83930.29691250.24113242336799
2.8393-2.93090.28551360.23343265340199
2.9309-3.03560.25971490.23033242339199
3.0356-3.15710.3281380.225232973435100
3.1571-3.30070.25831510.210332623413100
3.3007-3.47460.26231400.187632943434100
3.4746-3.69220.23271500.17133103460100
3.6922-3.9770.22181320.164333323464100
3.977-4.37680.2011300.16533463476100
4.3768-5.0090.20231430.1533483491100
5.009-6.30650.2171530.183133983551100
6.3065-39.23030.21961420.196935703712100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0258-0.01990.010.06090.02080.0391-0.125-0.0514-0.2180.0970.11310.22280.0452-0.04140.037-0.02410.05840.10210.2085-0.08840.070730.9196-13.849710.6094
20.0181-0.0023-0.0020.01180.00040.0019-0.02460.00560.05320.10110.0084-0.0808-0.0378-0.0364-0.00220.120.0627-0.08170.0648-0.02260.136539.602-1.40613.1025
30.00760.00910.00330.02890.01830.0269-0.03-0.0796-0.06940.06690.0597-0.01690.04670.02410.02120.07390.02850.03020.1871-0.01460.131742.5353-14.485414.3942
40.01950.0358-0.00910.0789-0.01080.0136-0.0327-0.0173-0.0127-0.00630.0382-0.0432-0.00060.01820.00430.21350.0124-0.06830.36130.03180.04746.9589-12.626119.9725
50.0104-0.0116-0.00130.0176-0.02240.0176-0.00630.00140.0151-0.0099-0.04120.0448-0.0433-0.0773-0.0285-0.02270.0497-0.05150.1907-0.11880.19626.7133-4.14022.1177
60.0146-0.00650.01620.0023-0.00480.01720.0303-0.0708-0.00290.07550.0120.11350.0289-0.0640.00530.11970.02550.04390.14140.01250.092219.7989-6.749719.3477
70.0079-0.00140.0010.02270.01550.00760.0019-0.0385-0.02380.02670.03850.0122-0.03020.01360.03390.14980.12070.20230.2656-0.12870.306915.9086-0.887320.4795
80.02510.0140.00130.01410.0210.0513-0.0861-0.0396-0.06650.0808-0.07020.09840.0658-0.0306-0.0909-0.22950.20840.22840.0446-0.16620.132217.0567-10.145514.5051
90.00570.00090.00490.0127-0.01050.01380.01060.0097-0.0187-0.0068-0.0166-0.02720.01380.0148-0.00860.05540.09330.09850.0778-0.1340.215727.4099-2.02436.1879
100.0536-0.00960.02160.01150.02160.01780.03710.0061-0.0157-0.08490.1298-0.0894-0.09050.25340.1461-0.16430.20190.2720.1299-0.2864-0.17223.66555.8949-15.6917
110.01590.0056-0.00470.014-0.0110.0120.0311-0.00490.01290.00850.0293-0.004-0.02240.09010.02940.0293-0.1109-0.03570.2455-0.15940.18130.84345.9683-7.9529
120.077-0.04360.02340.09310.04780.12370.06520.11930.1297-0.2313-0.0147-0.0543-0.20250.21220.0407-0.10520.06790.12470.1401-0.0854-0.11819.40767.4206-24.5335
130.0429-0.0322-0.09630.03070.0610.22490.11510.03990.0272-0.07170.02-0.0254-0.09250.07690.12720.0485-0.0278-0.07710.1328-0.2865-0.097718.303310.9982-26.4611
140.1479-0.0345-0.02680.049-0.04680.0880.00330.08610.033-0.03010.06090.01120.04-0.05860.02320.11380.10950.020.2425-0.05140.101959.9457-15.3055-9.4914
150.02420.031-0.03620.0425-0.03260.05940.07330.00380.1686-0.01020.02270.0345-0.02840.09010.015-0.15120.32840.1340.0081-0.19540.080264.6575-12.0824-0.2121
160.002-0.0009-0.00140.0043-0.00340.0080.0051-0.0275-0.00130.0176-0.00140.03890.01780.00150.01210.22130.21290.0730.1671-0.08680.125164.8951-20.92079.0535
170.0218-0.00360.00140.00420.00340.0075-0.00150.0291-0.008-0.0279-0.01-0.06060.03620.05570.0040.19830.07990.13020.176-0.12480.189672.4294-12.13073.751
180.0181-0.01260.01880.02290.00430.0509-0.0039-0.02610.02370.0243-0.0171-0.0424-0.05890.0327-0.01550.180.2016-0.03560.3308-0.15190.300478.669-15.56655.5548
190.04080.03180.02540.1487-0.07140.18270.06170.04940.0522-0.01590.10360.01540.0182-0.08010.05740.05360.02210.05380.2151-0.05820.143550.576-15.36311.6945
200.0017-0.0007-0.00310.0069-0.0022-0.00070.08570.1019-0.0411-0.07220.0001-0.02360.02860.05440.03020.12060.22160.08890.105-0.12550.022258.8897-27.5398-9.8209
210.0565-0.0476-0.00580.0643-0.01120.0390.03460.1376-0.1322-0.06650.01810.01420.1291-0.02680.07980.2001-0.05070.06190.3566-0.28230.079552.5725-25.4487-10.8726
220.0013-0.001-0.000300.00040.00060.00930.0021-0.0009-0.0170.0301-0.0221-0.00280.00030.01110.37610.05480.0870.405-0.12260.100765.4199-22.7085-14.9851
230.00240.00350.00080.0040.00310.0005-0.02050.0288-0.027-0.0224-0.02690.04570.0155-0.0309-0.01750.218-0.00440.04060.2668-0.32370.258251.6137-26.708-11.0322
240.01760.00530.00070.006400.0069-0.016-0.01570.05580.0071-0.0228-0.0034-0.00790.0113-0.02830.07180.09650.20490.0294-0.02630.264952.9849-19.40832.4177
250.09560.0219-0.05760.03180.00650.0414-0.03420.09280.05430.05770.04630.04120.1583-0.0246-0.00240.25450.048-0.07690.12180.00530.10483.4759-19.0478-27.711
260.00530.0005-0.00090.0127-0.00470.00450.0319-0.0598-0.0267-0.00350.00160.0460.05950.0097-0.00140.5837-0.0042-0.01430.33690.08960.11175.1732-18.4339-12.4538
270.01110.0051-0.00060.0082-0.00790.0091-0.0069-0.0118-0.0026-0.0148-0.0336-0.0345-0.01750.027-0.00180.31310.2367-0.12180.10670.00780.125614.229-16.9455-22.3468
28-0.00080.00620.00540.03110.00020.04160.0462-0.0631-0.00530.07550.0133-0.08420.12980.0575-00.21150.06980.02560.2389-0.00710.16770.8789-16.185-21.05
290.0086-0.01730.02040.0436-0.02990.04620.0741-0.0024-0.0872-0.01180.04060.03870.0762-0.02080.02780.3506-0.0613-0.01250.07010.1030.1486-4.5658-32.4323-25.1936
300.01720.01670.00490.0131-0.00190.0044-0.0243-0.0002-0.01880.0433-0.04550.04880.0911-0.0855-0.04040.336-0.2125-0.03110.08460.12930.2354-10.1397-29.5513-27.6543
310.0023-0.0004-0.00110.0007-0.00150.00310.01740.0111-0.01140.00830.0009-0.04930.0152-0.018500.47520.086-0.02550.29660.02040.26572.5343-33.0479-31.9289
320.04520.0141-0.03410.11160.00550.02340.0439-0.0514-0.00920.00720.03060.01240.0643-0.03350.01120.4257-0.08410.04120.21470.06810.1514-9.4195-24.8702-23.9039
330.00490.00290.00180.0024-0.00330.0076-0.00840.0247-0.0214-0.00630.0270.01320.0087-0.02740.02230.1851-0.04920.23370.1319-0.03430.319462.0985-8.385-20.1507
340.0585-0.02840.02980.0660.0260.05430.0902-0.08110.07530.06690.0902-0.0113-0.1110.08180.07920.39850.04350.24850.1274-0.04670.177963.63067.5444-16.7113
350.0003-0.00190.00210.0105-0.01310.01230.00170.04490.0074-0.02850.00850.0085-0.0516-0.0153-0.00530.48310.05460.29430.13630.21460.338566.693816.4102-24.4896
36-0.0007-0.0004-0.00230.00660.00250.0022-0.031-0.0222-0.00110.01350.0221-0.0132-0.0466-0.0267-00.4851-0.02640.23420.312-0.16970.3566.447113.8335-12.0025
370.00820.00250.00850.0048-0.00070.0239-0.0236-0.09840.07970.0941-0.0842-0.021-0.08870.0749-0.00230.35850.04580.12320.2186-0.03880.380367.822214.1082-16.2861
380.0807-0.0236-0.07810.03590.00770.09370.08630.1311-0.0085-0.03830.08430.1171-0.1159-0.2290.0574-0.09660.07170.43590.15290.1151-0.033855.921-1.8386-30.5502
390.0304-0.00480.02060.0035-0.00370.0140.0498-0.02710.03240.01490.04770.0162-0.0081-0.020.04970.15140.11570.14830.37960.03950.320250.6068-1.2834-23.8242
400.04420.01360.04390.00770.00630.04380.03370.03850.02620.00420.0671-0.0528-0.0488-0.02560.01340.1720.07770.1380.25340.05910.228663.13443.1804-31.7508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 78 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 94 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 107 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 132 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 149 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 150 through 161 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 204 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 205 through 215 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 77 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 94 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 181 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 215 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 24 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 56 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 57 through 77 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 78 through 94 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 95 through 107 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 108 through 132 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 133 through 149 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 150 through 181 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 182 through 192 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 193 through 204 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 205 through 215 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 56 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 57 through 78 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 79 through 94 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 95 through 132 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 133 through 149 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 150 through 181 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 182 through 192 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 193 through 215 )D0
33X-RAY DIFFRACTION33chain 'E' and (resid 1 through 16 )E0
34X-RAY DIFFRACTION34chain 'E' and (resid 17 through 56 )E0
35X-RAY DIFFRACTION35chain 'E' and (resid 57 through 77 )E0
36X-RAY DIFFRACTION36chain 'E' and (resid 78 through 94 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 95 through 118 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 119 through 181 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 182 through 201 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 202 through 215 )E0

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