6TW6

Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923

PDB DOI: https://doi.org/10.2210/pdb6TW6/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium vivax Sal-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-12 Released: 2021-07-21
Deposition Author(s): Brannigan, J.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.208
R-Value Work: 0.168

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923

Brannigan, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 140.81 kDa
Atom Count: 11,986
Modelled Residue Count: 1,137
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A [auth AAA], B [auth BBB], C [auth CCC]	388	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PVX_085815 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHW Query on NHW Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain J [auth BBB] SDF format, chain O [auth CCC] MOL2 format, chain D [auth AAA] MOL2 format, chain J [auth BBB] MOL2 format, chain O [auth CCC]	D [auth AAA], J [auth BBB], O [auth CCC]	2-oxopentadecyl-CoA C₃₆ H₆₄ N₇ O₁₇ P₃ S JKWHUJMJVNMKEF-UOCZADIYSA-J		Interactions Focus chain D [auth AAA] Focus chain J [auth BBB] Focus chain O [auth CCC] Interactions & Density Focus chain D [auth AAA] Focus chain J [auth BBB] Focus chain O [auth CCC]
NZE (Subject of Investigation/LOI) Query on NZE Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain K [auth BBB] SDF format, chain P [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain K [auth BBB] MOL2 format, chain P [auth CCC]	E [auth AAA], K [auth BBB], P [auth CCC]	[(5-{4-fluoro-2-[2-(1H-imidazol-1-yl)ethoxy]phenyl}-1H-indazol-3-yl)methyl]dimethylamine C₂₁ H₂₂ F N₅ O YRWJVRAKMIULHA-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain K [auth BBB] Focus chain P [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain K [auth BBB] Focus chain P [auth CCC]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] MOL2 format, chain G [auth AAA]	G [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth AAA] Interactions & Density Focus chain G [auth AAA]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain N [auth BBB] SDF format, chain S [auth CCC] SDF format, chain T [auth CCC] MOL2 format, chain I [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain S [auth CCC] MOL2 format, chain T [auth CCC]	I [auth AAA], N [auth BBB], S [auth CCC], T [auth CCC]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth AAA] Focus chain N [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Interactions & Density Focus chain I [auth AAA] Focus chain N [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain M [auth BBB] SDF format, chain R [auth CCC] MOL2 format, chain H [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain R [auth CCC]	H [auth AAA], M [auth BBB], R [auth CCC]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth AAA] Focus chain M [auth BBB] Focus chain R [auth CCC] Interactions & Density Focus chain H [auth AAA] Focus chain M [auth BBB] Focus chain R [auth CCC]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain L [auth BBB] SDF format, chain Q [auth CCC] MOL2 format, chain F [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain Q [auth CCC]	F [auth AAA], L [auth BBB], Q [auth CCC]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain L [auth BBB] Focus chain Q [auth CCC] Interactions & Density Focus chain F [auth AAA] Focus chain L [auth BBB] Focus chain Q [auth CCC]