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- PDB-3kku: Cruzain in complex with a non-covalent ligand -

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Basic information

Entry
Database: PDB / ID: 3kku
TitleCruzain in complex with a non-covalent ligand
ComponentsCruzipain
KeywordsHYDROLASE / Autocatalytic cleavage / Glycoprotein / Protease / Thiol protease / Zymogen
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-B95 / S-methyl methanesulfonothioate / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsFerreira, R.S. / Eidam, O. / Shoichet, B.K.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.
Authors: Ferreira, R.S. / Simeonov, A. / Jadhav, A. / Eidam, O. / Mott, B.T. / Keiser, M.J. / McKerrow, J.H. / Maloney, D.J. / Irwin, J.J. / Shoichet, B.K.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,83613
Polymers22,7151
Non-polymers1,12112
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.978, 82.978, 101.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

21A-278-

HOH

31A-372-

HOH

41A-422-

HOH

51A-537-

HOH

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P25779, cruzipain
#2: Chemical ChemComp-B95 / N-[2-(1H-benzimidazol-2-yl)ethyl]-2-(2-bromophenoxy)acetamide


Mass: 374.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16BrN3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-Z22 / S-methyl methanesulfonothioate / S-Methyl methanethiosulfonate


Mass: 126.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 2.0 M NH4H2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 59354 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 7.93 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 78
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 11 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 29.3 / Num. unique all: 5282 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I06

3i06


Resolution: 1.28→30.668 Å / SU ML: 0.3 / σ(F): 1.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.144 2725 5.08 %
Rwork0.1147 --
obs0.1162 53676 53.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.849 Å2 / ksol: 0.368 e/Å3
Refinement stepCycle: LAST / Resolution: 1.28→30.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 65 310 1967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131771
X-RAY DIFFRACTIONf_angle_d1.4912417
X-RAY DIFFRACTIONf_dihedral_angle_d19.089614
X-RAY DIFFRACTIONf_chiral_restr0.096261
X-RAY DIFFRACTIONf_plane_restr0.009314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.3030.13161430.07772610X-RAY DIFFRACTION52
1.303-1.32810.131410.0812644X-RAY DIFFRACTION52
1.3281-1.35520.13481290.07622660X-RAY DIFFRACTION52
1.3552-1.38470.11651290.07842644X-RAY DIFFRACTION52
1.3847-1.41690.12981550.0822622X-RAY DIFFRACTION52
1.4169-1.45230.12481560.08952648X-RAY DIFFRACTION52
1.4523-1.49160.13511290.08422644X-RAY DIFFRACTION52
1.4916-1.53540.12661330.08372659X-RAY DIFFRACTION53
1.5354-1.5850.12981590.08622623X-RAY DIFFRACTION53
1.585-1.64170.12271360.0912676X-RAY DIFFRACTION53
1.6417-1.70740.11821500.09862656X-RAY DIFFRACTION53
1.7074-1.78510.13731380.10042668X-RAY DIFFRACTION53
1.7851-1.87920.13161440.09792686X-RAY DIFFRACTION53
1.8792-1.99690.12681540.09782686X-RAY DIFFRACTION53
1.9969-2.1510.13471410.10522697X-RAY DIFFRACTION53
2.151-2.36740.14311410.11122700X-RAY DIFFRACTION54
2.3674-2.70980.16711420.13182748X-RAY DIFFRACTION54
2.7098-3.41340.14861580.13222766X-RAY DIFFRACTION55
3.4134-30.67660.15271470.13682914X-RAY DIFFRACTION57

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