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- PDB-7s19: Crystal structure of cruzain with gallinamide analog from 2-indol... -

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Basic information

Entry
Database: PDB / ID: 7s19
TitleCrystal structure of cruzain with gallinamide analog from 2-indolyl series
ComponentsCruzipain
KeywordsHYDROLASE / Cycteine Protease / Cruzain / Gallinamide
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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / Chem-83K / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsSharma, V. / Podust, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI127505 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi .
Authors: Barbosa Da Silva, E. / Sharma, V. / Hernandez-Alvarez, L. / Tang, A.H. / Stoye, A. / O'Donoghue, A.J. / Gerwick, W.H. / Payne, R.J. / McKerrow, J.H. / Podust, L.M.
History
DepositionSep 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)23,5002
Polymers22,7151
Non-polymers7851
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.930, 95.930, 68.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: P25779, cruzipain
#2: Chemical ChemComp-83K / N,N-dimethyl-L-valyl-L-leucyl-N-[(3S)-6-{(2S)-2-[(1H-indol-3-yl)methyl]-3-methoxy-5-oxo-2,5-dihydro-1H-pyrrol-1-yl}-6-oxo-1-phenylhexan-3-yl]-L-leucinamide


Mass: 785.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H64N6O6 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002487
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.03 Å3/Da / Density % sol: 69.45 %
Description: Transparent Rosettes of needle shaped crystals.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 800mM Potassium Phosphate, pH 8.0; 100mM Calcium Chloride; Betaine hydrochloride

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2021 / Details: Mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.08→83.08 Å / Num. obs: 22026 / % possible obs: 98.9 % / Redundancy: 19.676 % / Biso Wilson estimate: 42.284 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.42 / Rrim(I) all: 0.431 / Χ2: 0.715 / Net I/σ(I): 8.37 / Num. measured all: 433389 / Scaling rejects: 350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.08-2.1416.5945.5580.5423364163114080.1585.72186.3
2.14-2.220.3214.2610.8731904157015700.3484.369100
2.2-2.2619.9632.8861.1530304153115180.6722.96199.2
2.26-2.3319.194.5120.9229227152615230.4944.63499.8
2.33-2.419.8472.4761.728818145214520.5962.541100
2.4-2.4920.7891.9742.2928731138213820.6822.023100
2.49-2.5820.521.6842.7328133137213710.7881.72799.9
2.58-2.6920.1591.4753.226348130713070.8291.513100
2.69-2.8119.2671.1084.3524277126012600.911.138100
2.81-2.9519.6890.816.223903121412140.9490.832100
2.95-3.120.7230.5928.523707114411440.9790.606100
3.1-3.2920.5220.42511.1722615110211020.9890.436100
3.29-3.5220.0550.28615.1420175100610060.9940.293100
3.52-3.818.7750.24317.45181559679670.9950.25100
3.8-4.1620.5850.16722.42181978848840.9970.171100
4.16-4.6620.1620.1226.65162918088080.9980.123100
4.66-5.3818.5750.12124.73134307237230.9980.125100
5.38-6.5919.520.12425.04118686086080.9980.127100
6.59-9.3118.7320.08829.6891604894890.9990.09100
9.31-83.0816.490.0732.8947822942900.9990.07298.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kku

3kku


Resolution: 2.08→83.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.138 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1056 4.9 %RANDOM
Rwork0.2002 ---
obs0.2025 20511 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.02 Å2 / Biso mean: 39.271 Å2 / Biso min: 23.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.08→83.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 57 79 1728
Biso mean--46.45 39.75 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191695
X-RAY DIFFRACTIONr_bond_other_d0.0020.021515
X-RAY DIFFRACTIONr_angle_refined_deg2.1731.9532324
X-RAY DIFFRACTIONr_angle_other_deg1.08533485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.87125.73568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24615231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.09153
X-RAY DIFFRACTIONr_chiral_restr0.1110.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
LS refinement shellResolution: 2.083→2.137 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 83 -
Rwork0.377 1325 -
all-1408 -
obs--86.27 %

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