Structure of prolinyl-5'-O-adenosine phosphoramidate

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).

Ligands and binding sites

• V2P · (2~{S})-1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]pyrrolidine-2-carboxylic acid · ligand · chains B
• K · Potassium ion · metal · chains A
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 344 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

• 6XHD · Structure of Prolinyl-5'-O-adenosine phosphoramidate · the same entry in another collection · chain A against A, TM-score 1.00
• P61823 · AlphaFold monomer V2.0 prediction for ribonuclease pancreatic (P61823) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P61823
• Elsewhere: RCSB PDB 6XHD · PDBe 6XHD · UniProt P61823