MolNFT v1 · #135543 · protein
Crystal structure of a dihydrolipoyl dehydrogenase from neisseria gonorrhoeae bound to FAD
5U25 · Dihydrolipoamide dehydrogenase (E3 component of pyruvate…: “Crystal structure of a dihydrolipoyl dehydrogenase from neisseria gonorrhoeae bound to FAD”. X-ray diffraction, 2 ligands (FAD, SO4), 6 pockets (best druggability 0.79).…
- PDB
- 5U25
- Type
- protein
- Length
- 478 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoamide dehydrogenase (E3 component of pyruvate and 2-oxoglutarate dehydrogenase…
- EC
- 1.8.1.4
- UniProt
- A0A1D3G1L2
- Ligands
- FAD, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoamide dehydrogenase (E3 component of pyruvate and 2-oxoglutarate dehydrogenase complexes) (EC 1.8.1.4) | protein | 478 | 36% helix, 27% strand | A0A1D3G1L2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.79 | 0.81 | 95 | FAD, EDO |
| 2 | 257 | 0.56 | 0.77 | 27 | SO4 |
| 3 | 83 | 0.39 | 0.77 | 13 | SO4 |
| 4 | 84 | 0.33 | 0.74 | 17 | empty |
| 5 | 62 | 0.29 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5U25 · Crystal structure of a dihydrolipoyl dehydrogenase from Neisseria gonorrhoeae bound to FAD · 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 A0A1D3G1L2
- Elsewhere: RCSB PDB 5U25 · PDBe 5U25 · UniProt A0A1D3G1L2
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