6TW5 | pdb_00006tw5

Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-917

PDB DOI: https://doi.org/10.2210/pdb6TW5/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium vivax
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: 1.55 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-917

Brannigan, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 141.01 kDa
Atom Count: 12,014
Modeled Residue Count: 1,137
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

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| 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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K1A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYA Query on MYA Download:Ideal Coordinates CCD File SDF format, chain L [auth BBB] SDF format, chain Q [auth CCC] SDF format, chain E [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain Q [auth CCC] MOL2 format, chain E [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain Q [auth CCC] mmCIF format, chain E [auth AAA]	E [auth AAA], L [auth BBB], Q [auth CCC]	TETRADECANOYL-COA C₃₅ H₆₂ N₇ O₁₇ P₃ S DUAFKXOFBZQTQE-QSGBVPJFSA-N		Interactions Focus chain E [auth AAA] Focus chain L [auth BBB] Focus chain Q [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain L [auth BBB] Focus chain Q [auth CCC]
9M2 (Subject of Investigation/LOI) Query on 9M2 Download:Ideal Coordinates CCD File SDF format, chain P [auth CCC] SDF format, chain K [auth BBB] SDF format, chain D [auth AAA] MOL2 format, chain P [auth CCC] MOL2 format, chain K [auth BBB] MOL2 format, chain D [auth AAA] mmCIF format, chain P [auth CCC] mmCIF format, chain K [auth BBB] mmCIF format, chain D [auth AAA]	D [auth AAA], K [auth BBB], P [auth CCC]	1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine C₂₄ H₂₈ F N₅ O CGEINWMYWNHNPM-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain K [auth BBB] Focus chain P [auth CCC] Interactions & Density Focus chain D [auth AAA] Focus chain K [auth BBB] Focus chain P [auth CCC]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth CCC] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] MOL2 format, chain U [auth CCC] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain U [auth CCC] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA], J [auth AAA], U [auth CCC]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain U [auth CCC] Interactions & Density Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain U [auth CCC]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain S [auth CCC] SDF format, chain N [auth BBB] SDF format, chain G [auth AAA] MOL2 format, chain S [auth CCC] MOL2 format, chain N [auth BBB] MOL2 format, chain G [auth AAA] mmCIF format, chain S [auth CCC] mmCIF format, chain N [auth BBB] mmCIF format, chain G [auth AAA]	G [auth AAA], N [auth BBB], S [auth CCC]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain N [auth BBB] Focus chain S [auth CCC] Interactions & Density Focus chain G [auth AAA] Focus chain N [auth BBB] Focus chain S [auth CCC]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth CCC] SDF format, chain O [auth BBB] SDF format, chain H [auth AAA] MOL2 format, chain T [auth CCC] MOL2 format, chain O [auth BBB] MOL2 format, chain H [auth AAA] mmCIF format, chain T [auth CCC] mmCIF format, chain O [auth BBB] mmCIF format, chain H [auth AAA]	H [auth AAA], O [auth BBB], T [auth CCC]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth AAA] Focus chain O [auth BBB] Focus chain T [auth CCC] Interactions & Density Focus chain H [auth AAA] Focus chain O [auth BBB] Focus chain T [auth CCC]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth CCC] SDF format, chain M [auth BBB] SDF format, chain F [auth AAA] MOL2 format, chain R [auth CCC] MOL2 format, chain M [auth BBB] MOL2 format, chain F [auth AAA] mmCIF format, chain R [auth CCC] mmCIF format, chain M [auth BBB] mmCIF format, chain F [auth AAA]	F [auth AAA], M [auth BBB], R [auth CCC]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain M [auth BBB] Focus chain R [auth CCC] Interactions & Density Focus chain F [auth AAA] Focus chain M [auth BBB] Focus chain R [auth CCC]