X-ray structure of the desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)

Structure

x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).

Ligands and binding sites

• FEC · 1,3,5,8-tetramethyl-porphine-2,4,6,7-tetrapropionic acid ferrous complex · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
• FE · Fe (III) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
• SO4 · Sulfate ion · ion · 34 copies · chains A, B, C, D, E, F, G, H, I, J, K, P, L, M, N, O
• GOL · Glycerol · additive · chains K, P

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

30 interfaces between chains.

• A–B · 1725 Ų buried · 20 hydrogen bonds · protein-protein
• I–J · 1702 Ų buried · 18 hydrogen bonds · protein-protein
• M–N · 1700 Ų buried · 15 hydrogen bonds · protein-protein
• C–D · 1691 Ų buried · 19 hydrogen bonds · protein-protein
• G–H · 1687 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

• 1NF6 · X-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in… · the same entry in another collection · chain K against K, 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 Q93PP9
• Elsewhere: RCSB PDB 1NF6 · PDBe 1NF6 · UniProt Q93PP9