Crystal structure of active site mutant C55A of nitrile reductase quef, bound to substrate PREQ0

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 33% strand (DSSP).

Ligands and binding sites

• PQ0 · 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile · ligand · 4 copies · chains A, B, C, D, E
• CA · Calcium ion · metal · 8 copies · chains B, C, D, E
• PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A, B, C, D, E

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

Pockets

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

Interfaces

6 interfaces between chains.

• D–E · 1573 Ų buried · 27 hydrogen bonds · protein-protein
• A–B · 1500 Ų buried · 24 hydrogen bonds · protein-protein
• B–C · 1497 Ų buried · 22 hydrogen bonds · protein-protein
• C–D · 1494 Ų buried · 26 hydrogen bonds · protein-protein
• A–E · 512 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 4FGC · Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to… · the same entry in another collection · chain D against D, TM-score 1.00
• O31678 · AlphaFold monomer V2.0 prediction for NADPH-dependent 7-cyano-7-deazaguanine reductase… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O31678
• Elsewhere: RCSB PDB 4FGC · PDBe 4FGC · UniProt O31678