Insights into substrate binding at femo-cofactor in nitrogenase from the structure of an alpha-70ILE mofe protein variant

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).

Ligands and binding sites

• HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, C
• CFN · FE(7)-Mo-S(9)-N cluster · ligand · 2 copies · chains A, C
• CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, C, D
• CA · Calcium ion · metal · 2 copies · chains B, C, D, A

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 4750 Ų buried · 61 hydrogen bonds · protein-protein
• A–B · 4642 Ų buried · 56 hydrogen bonds · protein-protein
• B–D · 3156 Ų buried · 58 hydrogen bonds · protein-protein
• B–C · 1405 Ų buried · 18 hydrogen bonds · protein-protein
• A–D · 1377 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 3K1A · Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an… · the same entry in another collection · chain A against A, TM-score 1.00
• P07328 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein alpha chain… · a predicted model of the same protein · chain C against A, TM-score 1.00
• P07329 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein beta chain… · 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 P07328
• Every structure of UniProt P07329
• Elsewhere: RCSB PDB 3K1A · PDBe 3K1A · UniProt P07328 · UniProt P07329