5V0W

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001088

PDB DOI: https://doi.org/10.2210/pdb5V0W/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Plasmodium vivax
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-28 Released: 2018-03-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.184
R-Value Work: 0.147
R-Value Observed: 0.147

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Plasmodium vivax N-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy

Mendez, A., Bolling, C., Taylor, S., Makumire, S., Staker, B., Reers, A., Hammerson, B., Mayclin, S.J., Abendroth, J., Lorimer, D.D., Edwards, T.E., Tate, E.W., Subramanian, S., Bell, A.S., Myler, P.J., Asojo, O.A., Chakafana, G.

(2025) Acta Crystallogr F Struct Biol Commun 81: 1-10

DOI: https://doi.org/10.1107/S2053230X24011348

Macromolecule Content

Total Structure Weight: 147.28 kDa
Atom Count: 11,627
Modelled Residue Count: 1,147
Deposited Residue Count: 1,215
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A, B, C	405	Plasmodium vivax	Mutation(s): 0 Gene Names: PVC01_130042700, PVP01_1336100 EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I)) Explore A5K1A2 Go to UniProtKB: A5K1A2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5K1A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYA Query on MYA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain S [auth C] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain S [auth C] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain S [auth C] mmCIF format, chain K [auth B]	D [auth A], K [auth B], S [auth C]	TETRADECANOYL-COA C₃₅ H₆₂ N₇ O₁₇ P₃ S DUAFKXOFBZQTQE-QSGBVPJFSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C]
KFK Query on KFK Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B], T [auth C]	1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine C₂₅ H₂₉ F₂ N₅ O SOXNKJCQBRQUMS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth B] F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	J [auth A], Q [auth B], R [auth B], X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.184
R-Value Work: 0.147
R-Value Observed: 0.147
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.32	α = 90
b = 119.13	β = 90
c = 176.61	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-01-15
Changes: Database references, Structure summary