Guanylylpyridinol (gp)-bound hcgf from methanocaldococcus jannaschii

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 24% strand (DSSP).

Ligands and binding sites

• ZGP · 5'-O-[(R)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxo-2-sulfanylethyl)pyridin-4-yl]oxy}phosphoryl]guanosine · ligand · chains A, B
• FEG · 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine · ligand · chains A, B
• SO4 · Sulfate ion · ion · 6 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1093 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 3WVC · Guanylylpyridinol (GP)-bound HcgF from Methanocaldococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
• Q58649 · AlphaFold monomer V2.0 prediction for UPF0254 protein MJ1251 (Q58649) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q58649
• Elsewhere: RCSB PDB 3WVC · PDBe 3WVC · UniProt Q58649