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- PDB-4b13: Plasmodium vivax N-myristoyltransferase with a bound benzofuran i... -

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Basic information

Entry
Database: PDB / ID: 4b13
TitlePlasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25)
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / MALARIA / DRUG DESIGN
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
2-oxopentadecyl-CoA / Chem-X25 / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPLASMODIUM VIVAX (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsYu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Antimalarial Drug Discovery.
Authors: Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J.
History
DepositionJul 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 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 / 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_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_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.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
B: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
C: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,65216
Polymers135,2333
Non-polymers4,41913
Water20,7711153
1
A: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5195
Polymers45,0781
Non-polymers1,4414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6156
Polymers45,0781
Non-polymers1,5375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5195
Polymers45,0781
Non-polymers1,4414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.320, 119.130, 178.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE


Mass: 45077.594 Da / Num. of mol.: 3 / Fragment: RESIDUES 27-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax)
Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 6 types, 1166 molecules

#2: Chemical ChemComp-X25 / 4-{[2-(3-benzyl-1,2,4-oxadiazol-5-yl)-3-methyl-1-benzofuran-4-yl]oxy}piperidine


Mass: 389.447 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H23N3O3
#3: Chemical ChemComp-NHW / 2-oxopentadecyl-CoA


Mass: 991.916 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H64N7O17P3S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details4-{[2-(3-BENZYL-1,2, 4-OXADIAZOL-5-YL)-3-METHYL-1- BENZOFURAN-4-YL]OXY}PIPERIDINE (X25)
Sequence detailsMET26 EQUIVALENT TO ILE26 IN UNIPROT ACCESSION A5K1A2

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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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM SULPHATE, 24-26% PEG 3350, 0.1 M BISTRIS PH 6.0 - 6.5

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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: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.58→37 Å / Num. obs: 163266 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B10

4b10


Resolution: 1.58→37.51 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.88 / SU B: 2.808 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29113 8223 5 %RANDOM
Rwork0.23758 ---
obs0.24027 155636 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.261 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--0.72 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.58→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9408 0 290 1153 10851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0210247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6341.98413979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84251211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42324.499489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.284151793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3241543
X-RAY DIFFRACTIONr_chiral_restr0.150.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217718
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: 1.583→1.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 611 -
Rwork0.276 11370 -
obs--98.17 %

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