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- PDB-4a2z: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT... -

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Basic information

Entry
Database: PDB / ID: 4a2z
TitleCRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A PYRAZOLE SULPHONAMIDE LIGAND
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE / DRUG DISCOVERY
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
TETRADECANOYL-COA / Chem-VIQ / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsRobinson, D.A. / Brand, S. / Fairlamb, A.H. / Ferguson, M.A.J. / Frearson, J.A. / Wyatt, P.G.
Citation
Journal: J. Med. Chem. / Year: 2012
Title: Discovery of a novel class of orally active trypanocidal N-myristoyltransferase inhibitors.
Authors: Brand, S. / Cleghorn, L.A. / McElroy, S.P. / Robinson, D.A. / Smith, V.C. / Hallyburton, I. / Harrison, J.R. / Norcross, N.R. / Spinks, D. / Bayliss, T. / Norval, S. / Stojanovski, L. / ...Authors: Brand, S. / Cleghorn, L.A. / McElroy, S.P. / Robinson, D.A. / Smith, V.C. / Hallyburton, I. / Harrison, J.R. / Norcross, N.R. / Spinks, D. / Bayliss, T. / Norval, S. / Stojanovski, L. / Torrie, L.S. / Frearson, J.A. / Brenk, R. / Fairlamb, A.H. / Ferguson, M.A. / Read, K.D. / Wyatt, P.G. / Gilbert, I.H.
#1: Journal: Nature / Year: 2010
Title: N-Myristoyltransferase Inhibitors as New Leads to Treat Sleeping Sickness.
Authors: Frearson, J.A. / Brand, S. / Mcelroy, S.P. / Cleghorn, L.A.T. / Smid, O. / Stojanovski, L. / Price, H.P. / Guther, M.L.S. / Torrie, L.S. / Robinson, D.A. / Hallyburton, I. / Mpamhanga, C.P. ...Authors: Frearson, J.A. / Brand, S. / Mcelroy, S.P. / Cleghorn, L.A.T. / Smid, O. / Stojanovski, L. / Price, H.P. / Guther, M.L.S. / Torrie, L.S. / Robinson, D.A. / Hallyburton, I. / Mpamhanga, C.P. / Brannigan, J.A. / Wilkinson, A.J. / Hodgkinson, M. / Hui, R. / Qiu, W. / Raimi, O.G. / Van Aalten, D.M.F. / Brenk, R. / Gilbert, I.H. / Read, K.D. / Fairlamb, A.H. / Ferguson, M.A.J. / Smith, D.F. / Wyatt, P.G.
History
DepositionSep 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: 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)51,9565
Polymers50,5131
Non-polymers1,4434
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.498, 90.977, 53.459
Angle α, β, γ (deg.)90.00, 114.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE / N-MYRISTOYL TRANSFERASE


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

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Non-polymers , 5 types, 208 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-VIQ / 4-METHOXY-2,3,6-TRIMETHYL-N-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)BENZENESULFONAMIDE


Mass: 337.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N3O3S
#4: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.27 Å3/Da / Density % sol: 45.9 % / Description: NONE
Crystal growpH: 5.5 / Details: 25.9%PEG1500,0.2M NACL, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 17977 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.8 / % possible all: 79.2

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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: 2.31→19.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.901 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.512 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22573 1312 7.3 %RANDOM
Rwork0.16066 ---
obs0.16547 16617 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.31→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 93 204 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9824819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84823.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89815555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4751522
X-RAY DIFFRACTIONr_chiral_restr0.1120.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212726
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_it1.0021.52067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88923361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.80431468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3874.51458
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: 2.307→2.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 71 -
Rwork0.211 906 -
obs--73.68 %

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