Nucleotide-induced asymmetry within ATPase activator ring drives S54- rnap interaction and ATP hydrolysis

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Ligands and binding sites

• 08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
• ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains L, X
• MG · Magnesium ion · metal · 20 copies · chains A, B, C, D, E, G, H, I, J, K, M, N, O, P, Q, S, T, U, V, W

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

40 interfaces between chains.

• B–C · 1780 Ų buried · 20 hydrogen bonds · protein-protein
• V–W · 1777 Ų buried · 18 hydrogen bonds · protein-protein
• J–K · 1775 Ų buried · 20 hydrogen bonds · protein-protein
• D–E · 1753 Ų buried · 22 hydrogen bonds · protein-protein
• P–Q · 1735 Ų buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 4LY6 · Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and… · the same entry in another collection · chain E against E, 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 O67198
• Elsewhere: RCSB PDB 4LY6 · PDBe 4LY6 · UniProt O67198