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- PDB-6w59: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC063) -

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Basic information

Entry
Database: PDB / ID: 6w59
TitleTrypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC063)
ComponentsMalic enzyme
KeywordsOXIDOREDUCTASE/Inhibitor / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


malate dehydrogenase (decarboxylating) (NAD+) activity / malate metabolic process / NAD binding / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain ...Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SZD / Malic enzyme
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMercaldi, G.F. / Fagundes, M. / Faria, J.N. / Cordeiro, A.T.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)16/14271-4 Brazil
Sao Paulo Research Foundation (FAPESP)18/22202-8 Brazil
Sao Paulo Research Foundation (FAPESP)16/03151-8 Brazil
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Trypanosoma cruzi Malic Enzyme Is the Target for Sulfonamide Hits from the GSK Chagas Box.
Authors: Mercaldi, G.F. / Eufrasio, A.G. / Ranzani, A.T. / do Nascimento Faria, J. / Mota, S.G.R. / Fagundes, M. / Bruder, M. / Cordeiro, A.T.
History
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 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

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Assembly

Deposited unit
A: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3213
Polymers61,6101
Non-polymers7112
Water4,846269
1
A: Malic enzyme
hetero molecules

A: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6426
Polymers123,2212
Non-polymers1,4214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area5620 Å2
ΔGint-8 kcal/mol
Surface area42450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.385, 73.385, 233.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Malic enzyme


Mass: 61610.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_11g406 / Plasmid: pET_SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2XFZ1
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SZD / 3,5-bis(fluoranyl)-~{N}-[3-[[4-(trifluoromethyloxy)phenyl]sulfamoyl]phenyl]benzamide


Mass: 472.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13F5N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.55 Å3/Da / Density % sol: 51.84 % / Mosaicity: 0.37 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 1.2-1.4 M Na3-Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 1.95→47.47 Å / Num. obs: 47202 / % possible obs: 99 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.581 / Num. measured all: 7929 / Num. unique obs: 2994 / CC1/2: 0.61 / Rpim(I) all: 0.384 / Rrim(I) all: 0.701 / Net I/σ(I) obs: 1.1 / % possible all: 90.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w29

6w29


Resolution: 1.95→47.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.171 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1581 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.134
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2297 4.9 %RANDOM
Rwork0.1914 ---
obs0.1923 44841 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.79 Å2 / Biso mean: 33.169 Å2 / Biso min: 19.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0 Å2
2--0.56 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 1.95→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4257 0 47 269 4573
Biso mean--42.6 36.42 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174144
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6525959
X-RAY DIFFRACTIONr_angle_other_deg1.3631.5779598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87522.063223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41415749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02917
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 144 -
Rwork0.33 2989 -
all-3133 -
obs--90.71 %

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