Research workbench
The refined structure of pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 ångströms resolution
Analyse The refined structure of pseudomonas putida lipoamide dehydrogenase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LVL
- Type
- protein
- Length
- 458 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoamide dehydrogenase
- EC
- 1.8.1.4
- UniProt
- P09063
- Ligands
- FAD, NAD
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoamide dehydrogenase (EC 1.8.1.4) | protein | 458 | 35% helix, 24% strand | P09063 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.78 | 0.80 | 102 | FAD, NAD |
| 2 | 174 | 0.49 | 0.77 | 30 | empty |
| 3 | 89 | 0.33 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1LVL · The refined structure of pseudomonas putida lipoamide dehydrogenase complexed with NAD+… · the same entry in another collection · chain A against A, TM-score 1.00
- P09063 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase (P09063) · 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 P09063
- Elsewhere: RCSB PDB 1LVL · PDBe 1LVL · UniProt P09063
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