MolNFT v1 · #35942 · protein
Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdo
2EQ7 · 2-oxoglutarate dehydrogenase E3 component: “Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdo”. X-ray diffraction, 2 ligands (FAD, NAD), 8 pockets (best druggability 0.81). MolNFT v1 #35942 on…
- PDB
- 2EQ7
- Type
- protein
- Length
- 941 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate dehydrogenase E3 component; 2-oxoglutarate dehydrogenase E2 component
- EC
- 1.8.1.4, 2.3.1.61
- UniProt
- Q5SLK6, Q5SLK5
- Ligands
- FAD, NAD
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate dehydrogenase E3 component (EC 1.8.1.4) | protein | 452 | 37% helix, 26% strand | Q5SLK6 |
| C | 2-oxoglutarate dehydrogenase E2 component (EC 2.3.1.61) | protein | 37 | 35% helix, 0% strand | Q5SLK5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.81 | 0.83 | 98 | FAD, NAD |
| 2 | 881 | 0.81 | 0.83 | 99 | FAD, NAD |
| 3 | 640 | 0.79 | 0.84 | 64 | empty |
| 4 | 474 | 0.77 | 0.85 | 42 | empty |
| 5 | 291 | 0.69 | 0.84 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3175 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2EQ7 · Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdo · 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 Q5SLK6
- Every structure of UniProt Q5SLK5
- Elsewhere: RCSB PDB 2EQ7 · PDBe 2EQ7 · UniProt Q5SLK6 · UniProt Q5SLK5
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