Crystal structure of TA1416,DNA-directed RNA polymerase subunit L, from thermoplasma acidophilum

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 28% strand (DSSP).

Ligands and binding sites

• SCN · Thiocyanate ion · ion · 3 copies · chains A, B, C, D
• ACY · Acetic acid · additive · chains A, B
• FMT · Formic acid · additive · 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, 1 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 1923 Ų buried · 22 hydrogen bonds · protein-protein
• A–B · 1808 Ų buried · 21 hydrogen bonds · protein-protein
• B–D · 304 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 214 Ų buried · 4 hydrogen bonds · protein-protein
• A–D · 170 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 1XPP · Crystal Structure of TA1416,DNA-directed RNA polymerase subunit L, from Thermoplasma… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HIC5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit L (Q9HIC5) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q9HIC5
• Elsewhere: RCSB PDB 1XPP · PDBe 1XPP · UniProt Q9HIC5