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

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Basic information

Entry
Database: PDB / ID: 6gnu
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-F5Z / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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)51,9853
Polymers50,5131
Non-polymers1,4722
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-16 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.309, 89.934, 52.884
Angle α, β, γ (deg.)90.000, 114.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 50513.254 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-F5Z / 4-[4-(1-methylpiperidin-4-yl)butyl]-~{N}-[6-(2-methylpropyl)quinolin-5-yl]benzenesulfonamide


Mass: 493.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H39N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
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: ID14-4 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.54→48 Å / Num. obs: 59093 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 21
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.9 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h5z

3h5z


Resolution: 1.54→44.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.372 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 2985 5.1 %RANDOM
Rwork0.1567 ---
obs0.1582 56088 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.51 Å2 / Biso mean: 18.18 Å2 / Biso min: 7.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.01 Å2
2---0.07 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.54→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 98 270 3705
Biso mean--16.63 28.17 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193545
X-RAY DIFFRACTIONr_bond_other_d0.0020.023319
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9844836
X-RAY DIFFRACTIONr_angle_other_deg1.5153.0027591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42923.669169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46915554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.531522
X-RAY DIFFRACTIONr_chiral_restr0.1480.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213950
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02831
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 182 -
Rwork0.211 3529 -
all-3711 -
obs--82.41 %

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