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- PDB-4w5c: Crystal structure analysis of cruzain with three Fragments: 1 (N-... -

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Basic information

Entry
Database: PDB / ID: 4w5c
TitleCrystal structure analysis of cruzain with three Fragments: 1 (N-(1H-benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide), 6 (2-amino-4,6-difluorobenzothiazole) and 9 (N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide).
ComponentsCruzipain
KeywordsHYDROLASE/HYDROLASE Inhibitor / Cysteine protease / cruzain / fragments-based drug discovery / mutagenesis / SPR / 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 / 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-3H5 / Chem-3H6 / 4,6-difluoro-1,3-benzothiazol-2-amine / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsTochowicz, A. / McKerrow, J.H. / Craik, C.S.
CitationJournal: To Be Published
Title: Applying Fragments Based- Drug Design to identify multiple binding modes on cysteine protease.
Authors: Tochowicz, A. / Lee, G.M. / Arkin, M.R. / Neitz, J. / McKerrow, J. / Craik, C.S.
History
DepositionAug 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)115,17111
Polymers113,7815
Non-polymers1,3906
Water36020
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3333
Polymers22,7561
Non-polymers5772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9422
Polymers22,7561
Non-polymers1861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1983
Polymers22,7561
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9422
Polymers22,7561
Non-polymers1861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7561
Polymers22,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.790, 137.790, 166.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22756.121 Da / Num. of mol.: 5 / Fragment: UNP residues 122-337 / Mutation: C25S
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-3H5 / N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide


Mass: 255.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13N5O
#3: Chemical ChemComp-3H6 / N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide


Mass: 321.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12FN5O
#4: Chemical ChemComp-3H7 / 4,6-difluoro-1,3-benzothiazol-2-amine


Mass: 186.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H4F2N2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 1.2M K/Na Tartrate / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 3.27→30 Å / Num. obs: 25366 / % possible obs: 98.4 % / Redundancy: 8.1 % / Biso Wilson estimate: 84.44 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8
Reflection shellRedundancy: 7.7 % / Mean I/σ(I) obs: 2.89 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
MOSFLMdata reduction
XSCALEdata scaling
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKU

3kku


Resolution: 3.27→29.98 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1013 4.01 %
Rwork0.193 --
obs0.195 25279 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.96 Å2
Refinement stepCycle: LAST / Resolution: 3.27→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 98 20 8074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018278
X-RAY DIFFRACTIONf_angle_d1.25511315
X-RAY DIFFRACTIONf_dihedral_angle_d16.6142753
X-RAY DIFFRACTIONf_chiral_restr0.0791235
X-RAY DIFFRACTIONf_plane_restr0.0061463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.44240.33261420.27043391X-RAY DIFFRACTION100
3.4424-3.65770.3351420.23623403X-RAY DIFFRACTION99
3.6577-3.93950.25881430.20723417X-RAY DIFFRACTION99
3.9395-4.33490.25361420.18673421X-RAY DIFFRACTION100
4.3349-4.95970.19521440.16183444X-RAY DIFFRACTION100
4.9597-6.23950.23081460.1933514X-RAY DIFFRACTION100
6.2395-29.97980.19841540.17783676X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.8522 Å / Origin y: 33.8031 Å / Origin z: 11.953 Å
111213212223313233
T0.6626 Å20.0324 Å20.0402 Å2-0.8128 Å2-0.0761 Å2--0.5316 Å2
L0.1698 °2-0.2181 °2-0.1365 °2-0.6787 °2-0.3386 °2--0.7717 °2
S0.0736 Å °-0.1669 Å °0.1194 Å °-0.0431 Å °0.0189 Å °-0.0133 Å °-0.1913 Å °-0.1309 Å °-0.096 Å °
Refinement TLS groupSelection details: ALL

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