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- PDB-3wsa: The Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proli... -

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Basic information

Entry
Database: PDB / ID: 3wsa
TitleThe Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proliferation and acts Synergistically with Posaconazole
ComponentsSqualene synthase
KeywordsTRANSFERASE / isoprenoids / drug discovery / human squalene synthase / SQ-109
Function / homology
Function and homology information


squalene synthase / farnesyl diphosphate metabolic process / squalene synthase [NAD(P)H] activity / Cholesterol biosynthesis / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum ...squalene synthase / farnesyl diphosphate metabolic process / squalene synthase [NAD(P)H] activity / Cholesterol biosynthesis / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding / membrane
Similarity search - Function
Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-RWZ / Squalene synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShang, N. / Li, Q. / Huang, C.H. / Oldfield, E. / Guo, R.T.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: SQ109, a new drug lead for Chagas disease.
Authors: Veiga-Santos, P. / Li, K. / Lameira, L. / de Carvalho, T.M. / Huang, G. / Galizzi, M. / Shang, N. / Li, Q. / Gonzalez-Pacanowska, D. / Hernandez-Rodriguez, V. / Benaim, G. / Guo, R.T. / ...Authors: Veiga-Santos, P. / Li, K. / Lameira, L. / de Carvalho, T.M. / Huang, G. / Galizzi, M. / Shang, N. / Li, Q. / Gonzalez-Pacanowska, D. / Hernandez-Rodriguez, V. / Benaim, G. / Guo, R.T. / Urbina, J.A. / Docampo, R. / de Souza, W. / Oldfield, E.
History
DepositionMar 5, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 13, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,05610
Polymers247,7346
Non-polymers1,3224
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8596
Polymers123,8673
Non-polymers9923
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-35 kcal/mol
Surface area38920 Å2
MethodPISA
3
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1984
Polymers123,8673
Non-polymers3311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-35 kcal/mol
Surface area38740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.750, 154.006, 90.615
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Squalene synthase / SQS / SS / FPP:FPP farnesyltransferase / Farnesyl-diphosphate farnesyltransferase


Mass: 41288.988 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 31-370 / Mutation: K248L, K315L, K318L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P37268, squalene synthase
#2: Chemical
ChemComp-RWZ / N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine


Mass: 330.551 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H38N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT (FDFT_HUMAN, P37268) SHOWS CONFLICT AT THIS POSITION: D -> N

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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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.2M sodium citrate, pH 8.2, 28% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 48462 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.8 / Num. unique all: 16426 / % possible all: 81.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZF

1ezf


Resolution: 2.9→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.261 2305 RANDOM
Rwork0.206 --
all-52014 -
obs-46281 -
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15964 0 96 219 16279
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.313

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