Structure of the unready oxidized form of [nife] hydrogenase

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, H, B, I
• F3S · FE3-S4 cluster · ligand · 2 copies · chains A, H, B, I
• FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains H, I
• NI · Nickel (II) ion · metal · 2 copies · chains H, I
• MG · Magnesium ion · metal · 2 copies · chains H, I
• H2S · Hydrosulfuric acid · ion · 4 copies · chains A, H, B, I
• PER · Peroxide ion · ion · 2 copies · chains H, I
• GOL · Glycerol · additive · 7 copies · chains A, H, B, I

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–H · 3650 Ų buried · 64 hydrogen bonds · protein-protein
• B–I · 3571 Ų buried · 59 hydrogen bonds · protein-protein
• A–I · 442 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 215 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 1YQ9 · Structure of the unready oxidized form of [NiFe] hydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
• P12944 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain H against A, TM-score 1.00
• P12943 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain B 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 P12943
• Every structure of UniProt P12944
• Elsewhere: RCSB PDB 1YQ9 · PDBe 1YQ9 · UniProt P12943 · UniProt P12944