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- PDB-6qdf: Leishmania major N-myristoyltransferase in complex with thienopyr... -

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Basic information

Entry
Database: PDB / ID: 6qdf
TitleLeishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000096
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / myristoylation / benzothiophene / Leishmania
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / metal ion binding / cytosol
Similarity search - Function
Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HWN / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.49 Å
AuthorsBrannigan, J.A.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Novel Thienopyrimidine Inhibitors of Leishmania N -Myristoyltransferase with On-Target Activity in Intracellular Amastigotes.
Authors: Bell, A.S. / Yu, Z. / Hutton, J.A. / Wright, M.H. / Brannigan, J.A. / Paape, D. / Roberts, S.M. / Sutherell, C.L. / Ritzefeld, M. / Wilkinson, A.J. / Smith, D.F. / Leatherbarrow, R.J. / Tate, E.W.
History
DepositionJan 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: 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
Revision 2.0Sep 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9604
Polymers48,5711
Non-polymers1,3893
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-27 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.519, 90.286, 53.010
Angle α, β, γ (deg.)90.00, 111.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 48571.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: NMT, LMJF_32_0080 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HWN / 3-[[6-tert-butyl-2-[methyl-[(3S)-1-methylpyrrolidin-3-yl]amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile


Mass: 386.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% PEG 1500, 0.2 M NACL, 0.1 M NA CACODYLATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.49→49 Å / Num. obs: 67622 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.5
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.49→49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.557 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 3365 5 %RANDOM
Rwork0.17246 ---
obs0.17442 64224 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.09 Å2
2--0.06 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.49→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 91 336 3781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.6885311
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.422.29214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11315653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3391525
X-RAY DIFFRACTIONr_chiral_restr0.1230.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023056
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it21.8471734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9792.7652186
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9982.1622118
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.825.9215986
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 280 -
Rwork0.319 4692 -
obs--99.62 %

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