Crystal structure of homoisocitrate dehydrogenase from thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).

Ligands and binding sites

• 48Y · (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid · ligand · 4 copies · chains A, B, C, D
• NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 30 copies · chains A, B, C, D
• GOL · Glycerol · additive · 24 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 2386 Ų buried · 34 hydrogen bonds · protein-protein
• C–D · 2385 Ų buried · 33 hydrogen bonds · protein-protein
• A–C · 419 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 416 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 208 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 4YB4 · Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex… · the same entry in another collection · chain A against A, TM-score 1.00
• Q72IW9 · AlphaFold monomer V2.0 prediction for homoisocitrate dehydrogenase (Q72IW9) · 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 Q72IW9
• Elsewhere: RCSB PDB 4YB4 · PDBe 4YB4 · UniProt Q72IW9