Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from pyrococcus horikoshii OT3 in complex with ribose-1,5- bisphosphate, AMP and gmp

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Ligands and binding sites

• RI2 · 1,5-di-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C
• AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
• G · Guanosine-5'-monophosphate · ligand · 2 copies · chains B, C
• K · Potassium ion · metal · 3 copies · chains A, B, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 737 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 735 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 734 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 5YGA · Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
• O57947 · AlphaFold monomer V2.0 prediction for ribose 1,5-bisphosphate isomerase (O57947) · 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 O57947
• Elsewhere: RCSB PDB 5YGA · PDBe 5YGA · UniProt O57947