Horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1- methylhexylformamide

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).

Ligands and binding sites

• NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
• NWH · N-[(2S)-heptan-2-yl]formamide · ligand · 4 copies · chains A, B, C, D
• NMH · (R)-N-(1-methyl-hexyl)-formamide · ligand · chains C, D
• ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
• MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B, C

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 1723 Ų buried · 32 hydrogen bonds · protein-protein
• A–B · 1708 Ų buried · 31 hydrogen bonds · protein-protein
• B–D · 255 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 164 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 59 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 5VN1 · horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide · the same entry in another collection · chain D against D, TM-score 1.00
• P00327 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase E chain (P00327) · a predicted model of the same protein · chain C 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 P00327
• Elsewhere: RCSB PDB 5VN1 · PDBe 5VN1 · UniProt P00327