Crystal structure of the covalent thioimide intermediate of unimodular nitrile reductase quef

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 34% strand (DSSP).

Ligands and binding sites

• GD1 · 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one · ligand · 4 copies · chains A, B, C, D, E
• MG · Magnesium ion · metal · 4 copies · chains B, C, D, E
• PO4 · Phosphate ion · ion · chains B
• PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains 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 · 1592 Ų buried · 25 hydrogen bonds · protein-protein
• B–C · 1521 Ų buried · 26 hydrogen bonds · protein-protein
• C–D · 1503 Ų buried · 25 hydrogen bonds · protein-protein
• A–B · 1480 Ų buried · 20 hydrogen bonds · protein-protein
• A–E · 566 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 4F8B · Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase… · the same entry in another collection · chain B against B, 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 4F8B · PDBe 4F8B · UniProt O31678