High-resolution structure of H2-activated anaerobically purified dm. baculatum [nifese]-hydrogenase after crystallization under air

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains S, L, T, M
• FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
• CA · Calcium ion · metal · 7 copies · chains S, L, T, M
• NI · Nickel (II) ion · metal · 2 copies · chains L, M
• H2S · Hydrosulfuric acid · ion · 2 copies · chains L, M
• CL · Chloride ion · ion · chains S
• GOL · Glycerol · additive · 4 copies · chains S, M

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• T–M · 3411 Ų buried · 64 hydrogen bonds · protein-protein
• S–L · 3370 Ų buried · 58 hydrogen bonds · protein-protein
• L–M · 267 Ų buried · 0 hydrogen bonds · protein-protein
• S–M · 240 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 4KN9 · High-resolution structure of H2-activated anaerobically purified Dm. baculatum… · the same entry in another collection · chain S against S, TM-score 1.00
• P13063 · AlphaFold monomer V2.0 prediction for periplasmic [nifese] hydrogenase small subunit… · a predicted model of the same protein · chain S against A, 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 P13063
• Every structure of UniProt C7LN88
• Elsewhere: RCSB PDB 4KN9 · PDBe 4KN9 · UniProt P13063 · UniProt C7LN88