Crystal structure of tartrate dehydrogenase from pseudomonas putida in complex with NADH, oxalate and metal ion

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).

Ligands and binding sites

• NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
• OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
• NH4 · Ammonium ion · ion · 4 copies · chains A, B, C, D
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 2716 Ų buried · 55 hydrogen bonds · protein-protein
• C–D · 2714 Ų buried · 58 hydrogen bonds · protein-protein
• A–C · 661 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 653 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 171 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 modified (engineered).

Compared structures

• 3FLK · Crystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH… · the same entry in another collection · chain B against B, TM-score 1.00
• Q51945 · AlphaFold monomer V2.0 prediction for tartrate DEHYDROGENASE/DECARBOXYLASE (Q51945) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q51945
• Elsewhere: RCSB PDB 3FLK · PDBe 3FLK · UniProt Q51945