Research workbench
Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8
Analyse Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EQ6
- Type
- protein
- Length
- 920 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
- EC
- 1.8.1.4
- UniProt
- Q5SLR0
- Ligands
- FAD
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component (EC 1.8.1.4) | protein | 460 | 35% helix, 28% strand | Q5SLR0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.83 | 0.85 | 80 | empty |
| 2 | 995 | 0.81 | 0.82 | 101 | FAD |
| 3 | 1022 | 0.80 | 0.82 | 104 | FAD |
| 4 | 107 | 0.59 | 0.86 | 21 | empty |
| 5 | 94 | 0.56 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3836 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2EQ6 · Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 · 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 Q5SLR0
- Elsewhere: RCSB PDB 2EQ6 · PDBe 2EQ6 · UniProt Q5SLR0
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