Crystal structure of LARP1-unique domain DM15 bound to M7GPPPC

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Ligands and binding sites

• MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · chains A
• 91P · [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 881 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 5V87 · Crystal structure of LARP1-unique domain DM15 bound to m7GpppC · the same entry in another collection · chain A against A, TM-score 1.00
• Q6PKG0 · AlphaFold monomer V2.0 prediction for la-related protein 1 (Q6PKG0) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q6PKG0
• Elsewhere: RCSB PDB 5V87 · PDBe 5V87 · UniProt Q6PKG0