Crystal structure of L-TRP/INDOLEAMINE 2,3-dioxygenagse 1 (HIDO1) complex with the jk-loop refined in the open conformation

Structure

x-ray diffraction · 3 distinct chains · 59% helix, 4% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• NFK · N'-Formylkynurenine · ligand · 4 copies · chains A, B, C, D
• TRP · Tryptophan · ligand · 3 copies · chains C, D, A
• OXY · Oxygen molecule · ion · 3 copies · chains A, B, D
• PO4 · Phosphate ion · ion · 2 copies · chains A, C
• CL · Chloride ion · ion · 2 copies · chains C, D
• GOL · Glycerol · additive · 21 copies · chains A, D, B, C

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

Pockets

19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–C · 305 Ų buried · 4 hydrogen bonds · protein-protein
• A–D · 272 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 75 Ų buried · 1 hydrogen bond · protein-protein
• A–B · 53 Ų buried · 1 hydrogen bond · protein-protein
• B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 7P0N · Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the… · the same entry in another collection · chain D against D, TM-score 1.00
• P14902 · AlphaFold monomer V2.0 prediction for indoleamine 2,3-dioxygenase 1 (P14902) · a predicted model of the same protein · chain A 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 P14902
• Elsewhere: RCSB PDB 7P0N · PDBe 7P0N · UniProt P14902