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- PDB-4ufv: Plasmodium vivax N-myristoyltransferase in complex with a pyridyl... -

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Basic information

Entry
Database: PDB / ID: 4ufv
TitlePlasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 18)
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / MYRISTOYLATION / MALARIA / INHIBITOR
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-31A / GLYCOLIC ACID / 2-oxopentadecyl-CoA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPLASMODIUM VIVAX (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.75 Å
AuthorsYu, Z. / Brannigan, J.A. / Rangachari, K. / Heal, W.P. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J.
CitationJournal: Medchemcomm / Year: 2015
Title: Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase
Authors: Yu, Z. / Brannigan, J.A. / Rangachari, K. / Heal, W.P. / Wilkinson, A.J. / Holder, A.A. / Leatherbarrow, R.J. / Tate, E.W.
History
DepositionMar 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 / _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)139,97521
Polymers135,2333
Non-polymers4,74218
Water21,0241167
1
A: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6537
Polymers45,0781
Non-polymers1,5756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6717
Polymers45,0781
Non-polymers1,5936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6517
Polymers45,0781
Non-polymers1,5736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.480, 118.990, 177.740
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)
Plasmid: PET28 DERIVATIVE / 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 , 8 types, 1185 molecules

#2: Chemical ChemComp-NHW / 2-oxopentadecyl-CoA


Mass: 991.916 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H64N7O17P3S
#3: Chemical ChemComp-31A / N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-benzamide


Mass: 367.442 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H25N3O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1167 / 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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6 / Details: 0.2M AS, 25% PEG 3350, 0.1M BIS-TRIS PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→99 Å / Num. obs: 121366 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.75→98.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.215 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23715 6077 5 %RANDOM
Rwork0.186 ---
obs0.18855 115190 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.75→98.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9448 0 305 1167 10920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0210485
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.031.97914290
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66851258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86924.425504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.237151848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6231546
X-RAY DIFFRACTIONr_chiral_restr0.1620.21534
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217968
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_it0.9920.9734768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5891.4556010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4231.0985717
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: 1.749→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 376 -
Rwork0.28 7363 -
obs--85.63 %

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