MolNFT v1 · #67163 · protein
The structure of dihydrolipoamide dehydrogenase from colwellia psychrerythraea 34H.
3IC9: “The structure of dihydrolipoamide dehydrogenase from colwellia psychrerythraea 34H.”. X-ray diffraction, 2 ligands (FAD, NA), 14 pockets (best druggability 0.87). MolNFT v1 #67163 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3IC9
- Type
- protein
- Length
- 1,926 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoamide dehydrogenase
- UniProt
- Q488E0
- Ligands
- FAD, NA
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Dihydrolipoamide dehydrogenase | protein | 481 | 35% helix, 27% strand | Q488E0 |
| C | Dihydrolipoamide dehydrogenase | protein | 483 | 35% helix, 27% strand | Q488E0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.87 | 0.88 | 72 | empty |
| 2 | 984 | 0.86 | 0.87 | 75 | empty |
| 3 | 746 | 0.81 | 0.85 | 92 | FAD |
| 4 | 950 | 0.80 | 0.82 | 98 | FAD |
| 5 | 1033 | 0.79 | 0.81 | 104 | FAD |
Interfaces
3 interfaces between chains.
- A–B · 4074 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 4066 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3IC9 · The structure of dihydrolipoamide dehydrogenase from Colwellia psychrerythraea 34H. · the same entry in another collection · 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 Q488E0
- Elsewhere: RCSB PDB 3IC9 · PDBe 3IC9 · UniProt Q488E0
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