Human N-myristoyltransferase 1 (MNT1) with myristoyl-CoA analogue X10 bound

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).

Ligands and binding sites

• 94Q · ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 9-(3-but-3-ynyl-1,2-diazirin-3-yl)nonanethioate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 928 Ų buried · 23 hydrogen bonds · protein-protein

Compared structures

• 5NPQ · Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound · 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 B against A, TM-score 1.00

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
• Elsewhere: RCSB PDB 5NPQ · PDBe 5NPQ · UniProt P30419