Model for thiostrepton binding to the ribosomal L11-RNA

Structure

solution nmr · 3 distinct chains · 37% helix, 18% strand (DSSP).

Ligands and binding sites

• QUA · 8-hydroxy-4-(1-hydroxyethyl)quinoline-2-carboxylic acid · ligand · chains A, B, C
• NH2 · Amino group · ion · chains C

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

3 interfaces between chains.

• A–B · 1638 Ų buried · 44 hydrogen bonds · protein-nucleic
• B–C · 213 Ų buried · 4 hydrogen bonds · protein-nucleic
• A–C · 179 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified, 2 covalent, 1 d-amino (nonstandard, covalent ligand, D-amino acid).

Compared structures

• 2JQ7 · Model for thiostrepton binding to the ribosomal L11-RNA · the same entry in another collection · chain A against A, TM-score 1.00
• 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain A against A, TM-score 0.86
• 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain A against A, TM-score 0.86
• P29395 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P29395) · a predicted model of the same protein · chain A against A, TM-score 0.83
• P0C8P8 · AlphaFold monomer V2.0 prediction for thiostrepton (P0C8P8) · a predicted model of the same protein · chain C against A, TM-score 0.22

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 P29395
• Every structure of UniProt P0C8P8
• Elsewhere: RCSB PDB 2JQ7 · PDBe 2JQ7 · UniProt P29395 · UniProt P0C8P8