Structure of a double methionine mutant of ni-fe hydrogenase

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, H, B, I, C, J
• F3S · FE3-S4 cluster · ligand · 3 copies · chains A, H, B, I, C, J
• FCO · Carbonmonoxide-(dicyano) iron · ligand · 3 copies · chains H, I, J
• NI · Nickel (II) ion · metal · 3 copies · chains H, I, J
• MG · Magnesium ion · metal · 3 copies · chains H, I, J
• PER · Peroxide ion · ion · 3 copies · chains H, I, J
• GOL · Glycerol · additive · 7 copies · chains H, A, C, B, I, J

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

Pockets

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

Interfaces

8 interfaces between chains.

• B–I · 3594 Ų buried · 55 hydrogen bonds · protein-protein
• A–H · 3583 Ų buried · 58 hydrogen bonds · protein-protein
• C–J · 3564 Ų buried · 56 hydrogen bonds · protein-protein
• I–C · 526 Ų buried · 8 hydrogen bonds · protein-protein
• H–C · 468 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 3CUR · Structure of a double methionine mutant of NI-FE hydrogenase · the same entry in another collection · chain J against J, TM-score 1.00
• P18188 · 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
• P18187 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain C 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 P18187
• Every structure of UniProt P18188
• Elsewhere: RCSB PDB 3CUR · PDBe 3CUR · UniProt P18187 · UniProt P18188