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- PDB-6eu5: Leishmania major N-myristoyltransferase with bound myristoyl-CoA ... -

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Basic information

Entry
Database: PDB / ID: 6eu5
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 / metal ion binding / cytoplasm
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-BXN / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49608302465 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
DepositionOct 27, 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 / pdbx_unobs_or_zero_occ_residues / 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)52,0063
Polymers50,5131
Non-polymers1,4922
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-16 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.770, 90.590, 53.420
Angle α, β, γ (deg.)90.000, 114.141, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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-BXN / 4-[3-[(8~{a}~{R})-3,4,6,7,8,8~{a}-hexahydro-1~{H}-pyrrolo[1,2-a]pyrazin-2-yl]propyl]-2,6-bis(chloranyl)-~{N}-methyl-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide


Mass: 514.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H33Cl2N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
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: 1.496→48.748 Å / Num. obs: 65618 / % possible obs: 96.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.630988436 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.036 / Rrim(I) all: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.496→1.522 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3245 / CC1/2: 0.751 / Rpim(I) all: 0.526 / Rrim(I) all: 0.744 / % possible all: 95.1

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Processing

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

3h5z


Resolution: 1.49608302465→48.7479801992 Å / SU ML: 0.165468736412 / Cross valid method: FREE R-VALUE / σ(F): 1.35027070076 / Phase error: 21.0274788376
RfactorNum. reflection% reflection
Rfree0.203371258908 3073 4.68352308232 %
Rwork0.169057663273 --
obs0.170690026844 65613 96.232143381 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.6128418489 Å2
Refinement stepCycle: LAST / Resolution: 1.49608302465→48.7479801992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 96 227 3677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006846564678283590
X-RAY DIFFRACTIONf_angle_d0.9055140058724904
X-RAY DIFFRACTIONf_chiral_restr0.0869536726191513
X-RAY DIFFRACTIONf_plane_restr0.00594428753457626
X-RAY DIFFRACTIONf_dihedral_angle_d4.323123678722157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4961-1.51950.2738013505441170.2216716673882795X-RAY DIFFRACTION94.6376340591
1.5195-1.54440.2912967610241570.226222621572778X-RAY DIFFRACTION95.2922077922
1.5444-1.5710.2544207953651250.2272316294132825X-RAY DIFFRACTION94.7334617855
1.571-1.59960.2658386460291370.2217873152572804X-RAY DIFFRACTION95.7045232672
1.5996-1.63030.2783655819341380.2129796786212837X-RAY DIFFRACTION95.6284153005
1.6303-1.66360.2648289838031420.2115203949082801X-RAY DIFFRACTION96.0195758564
1.6636-1.69980.2489033347771440.2112011500462801X-RAY DIFFRACTION95.8346892288
1.6998-1.73930.2328368165931410.1956191890562854X-RAY DIFFRACTION95.9628324255
1.7393-1.78280.2236917619261580.1765425622612831X-RAY DIFFRACTION96.700097056
1.7828-1.8310.252852405691410.1666296620172825X-RAY DIFFRACTION96.8964390722
1.831-1.88490.1878103613991580.1569502859142846X-RAY DIFFRACTION97.09114415
1.8849-1.94580.2044731476261640.1462591990652870X-RAY DIFFRACTION97.5562700965
1.9458-2.01530.2036563605321670.1415723764762832X-RAY DIFFRACTION96.9608794051
2.0153-2.0960.1601325442651010.1410577687072858X-RAY DIFFRACTION96.1026307243
2.096-2.19140.1774080495541310.1438241306332888X-RAY DIFFRACTION96.8870346598
2.1914-2.30690.1798107272571310.1450148098112902X-RAY DIFFRACTION97.5868725869
2.3069-2.45150.191875269514980.1575848945532942X-RAY DIFFRACTION97.5609756098
2.4515-2.64070.2220048014021170.1779762249862885X-RAY DIFFRACTION97.5942782835
2.6407-2.90640.2039411683991480.1770798058122871X-RAY DIFFRACTION97.0427515268
2.9064-3.32690.1966742048281620.1776014177842842X-RAY DIFFRACTION96.2820512821
3.3269-4.19120.1749374475551590.1612278207872774X-RAY DIFFRACTION94.4909793814
4.1912-48.77390.2094175585831370.1716542763442879X-RAY DIFFRACTION94.6641556811

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