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- PDB-7juj: Cruzain bound to Gallinamide inhibitor -

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Basic information

Entry
Database: PDB / ID: 7juj
TitleCruzain bound to Gallinamide inhibitor
ComponentsCruzipain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cysteine protease / Cruzain / Gallinamide / HYDROLASE / 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 ...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
gallinamide A, bound form / : / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSilva, E.B. / Sharma, V. / Alvarez, L.H. / Gerwick, W.H. / McKerrow, J.H. / 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
DepositionAug 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 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 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
F: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,40726
Polymers136,2916
Non-polymers4,11620
Water4,197233
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4666
Polymers22,7151
Non-polymers7515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3102
Polymers22,7151
Non-polymers5951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4666
Polymers22,7151
Non-polymers7515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3884
Polymers22,7151
Non-polymers6733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4666
Polymers22,7151
Non-polymers7515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3102
Polymers22,7151
Non-polymers5951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.850, 139.850, 163.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

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Components

#1: Protein
Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: S of CYS25 forms covalent bond with gallinamide / 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-GN9 / gallinamide A, bound form / (2S)-1-{[(2S)-1-({(2S)-5-[(2S)-3-methoxy-2-methyl-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]-5-oxopentan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]amino}-4-methyl-1-oxopentan-2-yl N,N-dimethyl-L-isoleucinate


Mass: 594.783 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H54N4O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.7
Details: 0.82 M Potassium phosphate, pH 9.7; 0.01 M Betaine hydrochloride

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: Liquid Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2020 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.2→9.84 Å / Num. obs: 82446 / % possible obs: 100 % / Observed criterion σ(I): 0.43 / Redundancy: 26.6 % / Biso Wilson estimate: 57.29 Å2 / CC1/2: 0.998 / Rsym value: 0.33 / Χ2: 99.8 / Net I/σ(I): 11.83
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 26.8 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 6011 / CC1/2: 0.212 / Rsym value: 8.826 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKU

3kku


Resolution: 2.2→9.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 18.884 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 4150 5 %RANDOM
Rwork0.2013 ---
obs0.2047 78166 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.34 Å2 / Biso mean: 64.595 Å2 / Biso min: 35.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2--1.32 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: final / Resolution: 2.2→9.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 266 233 10051
Biso mean--90.61 52.51 -
Num. residues----1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01910136
X-RAY DIFFRACTIONr_bond_other_d0.0010.029135
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.94213908
X-RAY DIFFRACTIONr_angle_other_deg0.8823.00320986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80151304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.12625.694418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.269151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7141521
X-RAY DIFFRACTIONr_chiral_restr0.0940.21552
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022268
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 281 -
Rwork0.431 5695 -
all-5976 -
obs--99.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7025-0.47690.49671.9885-1.13584.5642-0.006-0.13950.20470.1114-0.0272-0.103-0.46640.15690.03310.11870.00270.03790.0839-0.03550.0613147.12422.17320.718
22.32051.0989-1.1352.9308-1.10932.6465-0.04850.48870.0263-0.25010.21780.29060.236-0.7309-0.16930.11660.0108-0.03730.43110.00060.0493117.55-0.32623.519
32.04510.2811-0.75062.2766-0.23073.54730.05950.0661-0.09210.0716-0.0093-0.28660.33830.4886-0.05020.1570.0621-0.04280.2408-0.09650.11144.24161.4123.118
41.51780.2465-0.13612.65240.28562.34290.06830.06610.0906-0.0421-0.06450.2141-0.0396-0.4107-0.00380.06660.06660.00230.1659-0.03430.0569120.39160.5642.751
51.6105-1.0329-0.08972.82010.42741.49160.07770.2051-0.1386-0.2857-0.12420.1278-0.0132-0.05360.04660.1420.00290.0140.1141-0.02180.0298131.57828.6-12.66
64.4969-0.719-0.2581.8998-0.60743.52260.0508-0.2224-0.99290.00660.16660.33630.1729-0.363-0.21740.3285-0.008-0.04280.68270.16670.5947102.29920.058-2.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 215
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B1 - 215
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION3C1 - 215
6X-RAY DIFFRACTION3C301
7X-RAY DIFFRACTION4D1 - 215
8X-RAY DIFFRACTION4D301
9X-RAY DIFFRACTION5E1 - 215
10X-RAY DIFFRACTION5E301
11X-RAY DIFFRACTION6F1 - 215
12X-RAY DIFFRACTION6F301

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