Research workbench
Crystal structure of a dihydrolipoamide dehydrogenase from sinorhizobium meliloti 1021
Analyse Crystal structure of a dihydrolipoamide dehydrogenase from sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3URH
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- Q92LK0
- Ligands
- FAD, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 461 | 35% helix, 26% strand | Q92LK0 |
| B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 465 | 34% helix, 26% strand | Q92LK0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.83 | 0.89 | 61 | empty |
| 2 | 870 | 0.79 | 0.82 | 102 | FAD, EDO |
| 3 | 890 | 0.78 | 0.81 | 100 | FAD |
| 4 | 497 | 0.75 | 0.83 | 51 | empty |
| 5 | 186 | 0.73 | 0.90 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 3460 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3URH · Crystal structure of a dihydrolipoamide dehydrogenase from Sinorhizobium meliloti 1021 · 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 Q92LK0
- Elsewhere: RCSB PDB 3URH · PDBe 3URH · UniProt Q92LK0
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