MolNFT v1 · #24753 · protein
Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+
1V59 · Dihydrolipoamide dehydrogenase: “Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+”. X-ray diffraction, 3 ligands (FAD, NAD, PO4), 10 pockets (best druggability 0.86). MolNFT v1 #24753 on GenesisL1: 3D…
- PDB
- 1V59
- Type
- protein
- Length
- 956 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoamide dehydrogenase
- EC
- 1.8.1.4
- UniProt
- P09624
- Ligands
- FAD, NAD, PO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrolipoamide dehydrogenase (EC 1.8.1.4) | protein | 478 | 33% helix, 28% strand | P09624 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.86 | 0.91 | 40 | empty |
| 2 | 721 | 0.78 | 0.83 | 85 | FAD |
| 3 | 769 | 0.78 | 0.82 | 97 | FAD, NAD |
| 4 | 141 | 0.68 | 0.89 | 31 | empty |
| 5 | 68 | 0.67 | 0.94 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3929 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1V59 · Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+ · the same entry in another collection · chain A against A, TM-score 1.00
- P09624 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase, mitochondrial (P09624) · 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 P09624
- Elsewhere: RCSB PDB 1V59 · PDBe 1V59 · UniProt P09624
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