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- PDB-4pi3: Crystal structure analysis of cruzain bound to vinyl sulfone anal... -

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Basic information

Entry
Database: PDB / ID: 4pi3
TitleCrystal structure analysis of cruzain bound to vinyl sulfone analog of WRR-483 (WRR-666)
ComponentsCruzipain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cystein protease / cruzain / Chagas Disease / covalent inhibitor / vinyl sulfone derivative / analoge of WRR-483 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cruzipain / 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 / 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-2V5 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsTochowicz, A. / McKerrow, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Sharon Reed, UCSDU01AI077822 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Synthesis and Evaluation of Oxyguanidine Analogues of the Cysteine Protease Inhibitor WRR-483 against Cruzain.
Authors: Jones, B.D. / Tochowicz, A. / Tang, Y. / Cameron, M.D. / McCall, L.I. / Hirata, K. / Siqueira-Neto, J.L. / Reed, S.L. / McKerrow, J.H. / Roush, W.R.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references / Other / Structure summary
Revision 1.2Feb 10, 2016Group: Database references / Other
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...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_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 16, 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
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7444
Polymers45,5442
Non-polymers1,1992
Water8,269459
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3722
Polymers22,7721
Non-polymers6001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3722
Polymers22,7721
Non-polymers6001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.923, 38.669, 94.646
Angle α, β, γ (deg.)90.00, 113.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22772.186 Da / Num. of mol.: 2 / Fragment: UNP residues 122-337
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-2V5 / N-[(2S)-5-(carbamimidamidooxy)-1-oxo-1-{[(1E,3S)-5-phenyl-1-(phenylsulfonyl)pent-1-en-3-yl]amino}pentan-2-yl]-4-methylpiperazine-1-carboxamide


Mass: 599.745 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H41N7O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Magnesium acetate, 30% (+/-)-2-Methyl-2,4-Pentanediol and 0.1 M Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.27→63.62 Å / Num. obs: 114913 / % possible obs: 99.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKU

3kku


Resolution: 1.27→86.52 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.827 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19741 5804 5 %RANDOM
Rwork0.17391 ---
obs0.17507 109411 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.982 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.16 Å2
2--1.41 Å20 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.27→86.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 84 459 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.023356
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5061.944592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.97725.735136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.35315462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.737156
X-RAY DIFFRACTIONr_chiral_restr0.1630.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 391 -
Rwork0.427 7694 -
obs--96.18 %

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