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- PDB-1f2a: CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO A VINYL SULFONE DE... -

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Basic information

Entry
Database: PDB / ID: 1f2a
TitleCRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO A VINYL SULFONE DERIVED INHIBITOR (II)
ComponentsCRUZAIN
KeywordsHYDROLASE / cysteine protease / covalent inhibitor / vinyl sulfone derived / P1' pocket
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-VS2 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsBrinen, L.S. / Hansell, E. / Roush, W.R. / McKerrow, J.H. / Fletterick, R.J.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: A target within the target: probing cruzain's P1' site to define structural determinants for the Chagas' disease protease.
Authors: Brinen, L.S. / Hansell, E. / Cheng, J. / Roush, W.R. / McKerrow, J.H. / Fletterick, R.J.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Crystal Structure of Cruzain: a Therapeutic Target for Chagas' Disease
Authors: McGrath, M.E. / Eakin, A.E. / Engel, J.C. / McKerrow, J.H. / Craik, C.S. / Fletterick, R.J.
History
DepositionMay 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CRUZAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3142
Polymers22,7151
Non-polymers5991
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.990, 51.280, 45.400
Angle α, β, γ (deg.)90.00, 116.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRUZAIN / CRUZIPAIN / CRUZAINE


Mass: 22715.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: DH5ALPHA / Production host: Escherichia coli (E. coli)
References: UniProt: P25779, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-VS2 / 3-[N-[BENZYLOXYCARBONYL]-PHENYLALANINYL-AMINO]-5-PHENYL-PENTANE-1-SULFONYLMETHYLBENZENE


Mass: 598.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate; micro seeding, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12 mg/mlprotein1drop
22 mMbis tris1drop
30.6-1.0 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 24660 / Num. obs: 23603 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.5
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.191 / % possible all: 82.8
Reflection shell
*PLUS
% possible obs: 82.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementResolution: 1.6→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2319 -random
Rwork0.184 ---
all-27175 --
obs-23153 85.2 %-
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 43 81 1768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_improper_angle_d0.92
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.92

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