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- PDB-4c7h: Leismania major N-myristoyltransferase in complex with a peptidom... -

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Basic information

Entry
Database: PDB / ID: 4c7h
TitleLeismania major N-myristoyltransferase in complex with a peptidomimetic (-NH2) molecule
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / MYRISTOYLATION
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
COENZYME A / Chem-EN5 / Chem-ENF / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsOlaleye, T.O. / Brannigan, J.A. / Goncalves, V. / Roberts, S.M. / Leatherbarrow, R.J. / Wilkinson, A.J. / Tate, E.W.
CitationJournal: Org.Biomol.Chem. / Year: 2014
Title: Peptidomimetic Inhibitors of N-Myristoyltransferase from Human Malaria and Leishmaniasis Parasites.
Authors: Olaleye, T.O. / Brannigan, J.A. / Roberts, S.M. / Leatherbarrow, R.J. / Wilkinson, A.J. / Tate, E.W.
History
DepositionSep 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)50,6708
Polymers47,5101
Non-polymers3,1607
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.659, 91.131, 53.777
Angle α, β, γ (deg.)90.00, 113.85, 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


Mass: 47510.129 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Plasmid: MAC040-B01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS
References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 7 types, 547 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EN5 / N-(10-aminodecanoyl)-L-seryl-N-(2-cyclohexylethyl)-L-lysinamide


Mass: 511.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H53N5O4
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#6: Chemical ChemComp-ENF / N-{(5E)-10-[(9E)-tetradec-9-enoylamino]dec-5-enoyl}-L-seryl-N-(2-cyclohexylethyl)-L-lysinamide


Mass: 722.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H79N5O5
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.5 / Details: 28% PEG1450, 0.2M NACL, 0.1M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.4→23 Å / Num. obs: 83119 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.4→22.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.143 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. LIGANDS MODELLED AS A MIXTURE OF REACTANT (80 PER CENT) AND PRODUCT (20 PER CENT) MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.20492 4168 5 %RANDOM
Rwork0.1726 ---
obs0.17419 78921 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.38 Å2
2---0.32 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 207 540 4101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0193806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7372.0125200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70623.5180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9471527
X-RAY DIFFRACTIONr_chiral_restr0.1850.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212902
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 319 -
Rwork0.32 5813 -
obs--98.7 %

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