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- PDB-6ewf: Leishmania major N-myristoyltransferase with bound myristoyl-CoA ... -

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Basic information

Entry
Database: PDB / ID: 6ewf
TitleLeishmania major N-myristoyltransferase with bound myristoyl-CoA and inhibitor
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / N-Myristoyltransferase / selective inhibitor / parasite
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-31A / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53517331196 Å
AuthorsBrenk, R. / Kehrein, J. / Kersten, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: J.Med.Chem. / Year: 2019
Title: How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System.
Authors: Kersten, C. / Fleischer, E. / Kehrein, J. / Borek, C. / Jaenicke, E. / Sotriffer, C. / Brenk, R.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8593
Polymers50,5131
Non-polymers1,3452
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-16 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.390, 90.220, 52.530
Angle α, β, γ (deg.)90.000, 111.905, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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-31A / N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-benzamide


Mass: 367.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 1500 25 % Sodium chloride 0.2 M Sodium cacodylate 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 29, 2017
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.535→48.738 Å / Num. obs: 59058 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 17.9124762709 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.033 / Rrim(I) all: 0.048 / Net I/σ(I): 15.7
Reflection shellResolution: 1.535→1.562 Å / Redundancy: 3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2944 / CC1/2: 0.728 / Rpim(I) all: 0.468 / Rrim(I) all: 0.67 / % possible all: 99.3

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Processing

Software
NameVersionClassification
autoPROC1.1.7data processing
PHASER2.8.0phasing
Coot0.8.2model building
PHENIX1.12_2829refinement
XDSBUILT=20170615data reduction
XSCALEBUILT=20170615data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H5Z

3h5z


Resolution: 1.53517331196→48.7375284157 Å / SU ML: 0.159851328862 / Cross valid method: FREE R-VALUE / σ(F): 1.34348286107 / Phase error: 19.8399868833
RfactorNum. reflection% reflection
Rfree0.194393836774 2934 4.9682499365 %
Rwork0.169481692218 --
obs0.170764560134 59055 98.770697441 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.7235764534 Å2
Refinement stepCycle: LAST / Resolution: 1.53517331196→48.7375284157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 90 214 3658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01606101188953573
X-RAY DIFFRACTIONf_angle_d1.443821468534871
X-RAY DIFFRACTIONf_chiral_restr0.0873930029244511
X-RAY DIFFRACTIONf_plane_restr0.01018301489623
X-RAY DIFFRACTIONf_dihedral_angle_d2.787570142072953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5352-1.56030.2732011621791330.2354612829312675X-RAY DIFFRACTION99.1525423729
1.5603-1.58720.2190767300481330.2283281377232676X-RAY DIFFRACTION99.0828924162
1.5872-1.61610.2736309856981320.2235163358532658X-RAY DIFFRACTION99.2176386913
1.6161-1.64720.2583552297031510.2079098142892679X-RAY DIFFRACTION99.1590749825
1.6472-1.68080.2238406120711500.198010874362666X-RAY DIFFRACTION98.6685353889
1.6808-1.71740.2368981215341370.1961991672622666X-RAY DIFFRACTION99.5383522727
1.7174-1.75730.2488520529781240.1900031489662696X-RAY DIFFRACTION99.6466431095
1.7573-1.80130.2095377505091570.178377648972710X-RAY DIFFRACTION99.6524157108
1.8013-1.850.199013533341310.1681895994242683X-RAY DIFFRACTION99.3293328627
1.85-1.90440.2213119361751340.1624860613952683X-RAY DIFFRACTION99.6462681288
1.9044-1.96590.1843498363591270.1665132425482678X-RAY DIFFRACTION99.1166077739
1.9659-2.03620.2151371276981520.1613011009222682X-RAY DIFFRACTION99.2992291521
2.0362-2.11770.1774010928991300.1586493663642690X-RAY DIFFRACTION99.1561181435
2.1177-2.21410.1956008612831450.1625854557242674X-RAY DIFFRACTION98.3600837404
2.2141-2.33080.1794911288261590.1675640774052618X-RAY DIFFRACTION98.475177305
2.3308-2.47680.1989902876391470.1727093648212674X-RAY DIFFRACTION98.7399369968
2.4768-2.6680.2069506249251430.1757785411572672X-RAY DIFFRACTION98.6334968465
2.668-2.93650.1870994286681410.1752533973232663X-RAY DIFFRACTION98.007689619
2.9365-3.36130.1873873438781310.1655859537722633X-RAY DIFFRACTION97.2212451636
3.3613-4.23450.1604423273081270.1510080354352672X-RAY DIFFRACTION97.1537660535
4.2345-48.76210.1867548876181500.1619641781042673X-RAY DIFFRACTION97.0770288858

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