Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human ARF6 octapeptide and coenzyme a

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).

Ligands and binding sites

• 4PS · 4'-diphospho pantetheine · ligand · chains A, B
• MYR · Myristic acid · ligand · chains A, B
• 6NA · Hexanoic acid · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 873 Ų buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 lipid (covalent ligand, myristoylation).

Compared structures

• 7RK3 · Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to… · the same entry in another collection · chain A against A, TM-score 1.00
• P30419 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase 1 (P30419) · a predicted model of the same protein · chain A against A, TM-score 1.00
• P62330 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 6 (P62330) · a predicted model of the same protein · chain B against A, TM-score 0.46

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P30419
• Every structure of UniProt P62330
• Elsewhere: RCSB PDB 7RK3 · PDBe 7RK3 · UniProt P30419 · UniProt P62330