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- PDB-3iut: The Crystal Structure of Cruzain in Complex with a Tetrafluorophe... -

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Basic information

Entry
Database: PDB / ID: 3iut
TitleThe Crystal Structure of Cruzain in Complex with a Tetrafluorophenoxymethyl Ketone Inhibitor
ComponentsCruzipain
KeywordsHYDROLASE / mature domain / papain family cysteine protease / Autocatalytic cleavage / Disulfide bond / 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 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-KB2 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKerr, I.D. / Debnath, M. / Brinen, L.S.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors as promising new leads for chagas disease chemotherapy.
Authors: Brak, K. / Kerr, I.D. / Barrett, K.T. / Fuchi, N. / Debnath, M. / Ang, K. / Engel, J.C. / McKerrow, J.H. / Doyle, P.S. / Brinen, L.S. / Ellman, J.A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)24,1546
Polymers23,4981
Non-polymers6565
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.081, 51.451, 45.853
Angle α, β, γ (deg.)90.00, 115.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 23497.986 Da / Num. of mol.: 1 / Fragment: UNP residues 123-337 / Mutation: S49A, S172G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: cruzipain / Plasmid: pPiCZalpha C / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P25779, cruzipain
#2: Chemical ChemComp-KB2 / (3S)-3-(4-{(1S)-1,2-dimethyl-1-[(quinolin-6-ylmethyl)amino]propyl}-1H-1,2,3-triazol-1-yl)heptan-2-one


Mass: 407.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33N5O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 265 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20 % PEG 3000, 100mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2008
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 1.2→41.38 Å / Num. obs: 56657 / % possible obs: 97.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 7.81 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.1
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 6.2 / Num. unique all: 7468 / % possible all: 88.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0071refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ME3

1me3


Resolution: 1.2→38 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.068 / SU ML: 0.022 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15296 2880 5.1 %RANDOM
Rwork0.12713 ---
obs0.12846 53757 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.06 Å2
2--0.37 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.036 Å0.037 Å
Refinement stepCycle: LAST / Resolution: 1.2→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 46 265 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211761
X-RAY DIFFRACTIONr_bond_other_d0.0020.021112
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9372418
X-RAY DIFFRACTIONr_angle_other_deg1.1143.0072701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65725.8973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05415241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.23153
X-RAY DIFFRACTIONr_chiral_restr0.110.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212042
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02330
X-RAY DIFFRACTIONr_mcbond_it1.951.51115
X-RAY DIFFRACTIONr_mcbond_other1.1651.5465
X-RAY DIFFRACTIONr_mcangle_it2.76121788
X-RAY DIFFRACTIONr_scbond_it3.43646
X-RAY DIFFRACTIONr_scangle_it4.6194.5626
X-RAY DIFFRACTIONr_rigid_bond_restr1.76632873
X-RAY DIFFRACTIONr_sphericity_free11.5573265
X-RAY DIFFRACTIONr_sphericity_bonded6.86932822
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 170 -
Rwork0.176 3313 -
obs--81.32 %

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