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- PDB-6gnt: Crystal Structure of Leishmania major N-Myristoyltransferase (NMT... -

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Basic information

Entry
Database: PDB / ID: 6gnt
TitleCrystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a Quionlinyl aryl sulphonamide ligand
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / ACYLTRANSFERASE / DRUG DISCOVERY
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-F5Q / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRobinson, D.A. / Harrison, J.R. / Brand, S. / Smith, V.C. / Thompson, S. / Smith, A. / Davies, K. / Mok, N.Y. / Torrie, L.S. / Collie, I. ...Robinson, D.A. / Harrison, J.R. / Brand, S. / Smith, V.C. / Thompson, S. / Smith, A. / Davies, K. / Mok, N.Y. / Torrie, L.S. / Collie, I. / Hallyburton, I. / Norval, S. / Simeons, F.R.C. / Stojanovski, L. / Frearson, J.A. / Brenk, R. / Wyatt, P.G. / Gilbert, I.H. / Read, K.D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustWT077705 United Kingdom
Wellcome TrustWT094090 United Kingdom
Wellcome TrustWT083481 United Kingdom
CitationJournal: J. Med. Chem. / Year: 2018
Title: A Molecular Hybridization Approach for the Design of Potent, Highly Selective, and Brain-Penetrant N-Myristoyltransferase Inhibitors.
Authors: Harrison, J.R. / Brand, S. / Smith, V. / Robinson, D.A. / Thompson, S. / Smith, A. / Davies, K. / Mok, N. / Torrie, L.S. / Collie, I. / Hallyburton, I. / Norval, S. / Simeons, F.R.C. / ...Authors: Harrison, J.R. / Brand, S. / Smith, V. / Robinson, D.A. / Thompson, S. / Smith, A. / Davies, K. / Mok, N. / Torrie, L.S. / Collie, I. / Hallyburton, I. / Norval, S. / Simeons, F.R.C. / Stojanovski, L. / Frearson, J.A. / Brenk, R. / Wyatt, P.G. / Gilbert, I.H. / Read, K.D.
History
DepositionMay 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)49,0874
Polymers47,5101
Non-polymers1,5773
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-18 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.757, 90.843, 53.677
Angle α, β, γ (deg.)90.000, 114.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 47510.129 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 (E. coli)
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F5Q / 4-[4-(1-methylpiperidin-4-yl)butyl]-~{N}-(6-pyrrolidin-1-ylquinolin-5-yl)benzenesulfonamide


Mass: 506.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H38N4O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 26%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6 / PH range: 4.5-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 54836 / % possible obs: 98.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 25
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.2 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wsa

2wsa


Resolution: 1.6→19.97 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.782 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2781 5.1 %RANDOM
Rwork0.1677 ---
obs0.1693 51956 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 399.36 Å2 / Biso mean: 23.974 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.6→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 105 289 3729
Biso mean--19.06 35.41 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193554
X-RAY DIFFRACTIONr_bond_other_d0.0010.023313
X-RAY DIFFRACTIONr_angle_refined_deg2.3511.9854848
X-RAY DIFFRACTIONr_angle_other_deg2.29837626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77223.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19315551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.571522
X-RAY DIFFRACTIONr_chiral_restr0.2650.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213971
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02848
LS refinement shellResolution: 1.601→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 193 -
Rwork0.24 3404 -
all-3597 -
obs--87.5 %

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