Research workbench
1.72 ångström resolution crystal structure of 2-oxoglutarate dehydrogenase complex subunit dihydrolipoamide dehydrogenase from bordetella pertussis in complex with FAD
Analyse 1.72 ångström resolution crystal structure of 2-oxoglutarate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AON
- Type
- protein
- Length
- 946 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- Q7VZ16
- Ligands
- FAD, CA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 473 | 35% helix, 28% strand | Q7VZ16 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.82 | 0.84 | 72 | empty |
| 2 | 805 | 0.80 | 0.83 | 92 | FAD |
| 3 | 747 | 0.79 | 0.83 | 80 | FAD |
| 4 | 213 | 0.71 | 0.87 | 47 | empty |
| 5 | 95 | 0.63 | 0.89 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3965 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6AON · 1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehydrogenase Complex… · 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 Q7VZ16
- Elsewhere: RCSB PDB 6AON · PDBe 6AON · UniProt Q7VZ16
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