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- PDB-5age: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT... -

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Basic information

Entry
Database: PDB / ID: 5age
TitleCRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A BENZOMORPHOLINONE LIGAND
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / NMT / 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-M9M / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRobinson, D.A. / Spinks, D. / Smith, V.C. / Thompson, S. / Smith, A. / Torrie, L.S. / McElroy, S.P. / Brand, S. / Brenk, R. / Frearson, J.A. ...Robinson, D.A. / Spinks, D. / Smith, V.C. / Thompson, S. / Smith, A. / Torrie, L.S. / McElroy, S.P. / Brand, S. / Brenk, R. / Frearson, J.A. / Read, K.D. / Wyatt, P.G. / Gilbert, I.H.
CitationJournal: Chemmedchem / Year: 2015
Title: Development of Small-Molecule Trypanosoma Brucei N-Myristoyltransferase Inhibitors: Discovery and Optimisation of a Novel Binding Mode.
Authors: Spinks, D. / Smith, V. / Thompson, S. / Robinson, D.A. / Luksch, T. / Smith, A. / Torrie, L.S. / Mcelroy, S. / Stojanovski, L. / Norval, S. / Collie, I.T. / Hallyburton, I. / Rao, B. / ...Authors: Spinks, D. / Smith, V. / Thompson, S. / Robinson, D.A. / Luksch, T. / Smith, A. / Torrie, L.S. / Mcelroy, S. / Stojanovski, L. / Norval, S. / Collie, I.T. / Hallyburton, I. / Rao, B. / Brand, S. / Brenk, R. / Frearson, J.A. / Read, K.D. / Wyatt, P.G. / Gilbert, I.H.
History
DepositionJan 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)51,8893
Polymers50,5131
Non-polymers1,3752
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.024, 90.165, 52.966
Angle α, β, γ (deg.)90.00, 113.78, 90.00
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 / Fragment: RESIDUES 5-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-M9M / 4-[(5-methyl-1,2-oxazol-3-yl)methyl]-7-[4-(1-methylpiperidin-4-yl)butyl]-2H-1,4-benzoxazin-3(4H)-one


Mass: 397.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H31N3O3
#3: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 44.5 % / Description: NONE
Crystal growpH: 5.5 / Details: 25.9%PEG1500,0.2M NACL, 0.1M CACODYLATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 25800 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5Z

3h5z


Resolution: 2→19.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.421 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23516 1319 5.1 %RANDOM
Rwork0.17368 ---
obs0.17693 24432 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.722 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.04 Å2
2---0.07 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 92 185 3621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223541
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9824826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62223.743171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7721522
X-RAY DIFFRACTIONr_chiral_restr0.150.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212740
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_it1.1551.52069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95223364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.07531472
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5524.51462
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.998→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 84 -
Rwork0.221 1679 -
obs--86.04 %

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