Research workbench
Crystal structure of E. COLI tRNA-dihydrouridine synthase B (dusb)
Analyse Crystal structure of E. COLI tRNA-dihydrouridine synthase B (dusb) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EI9
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-dihydrouridine synthase B
- EC
- 1.3.1.-
- UniProt
- P0ABT7
- Ligands
- FMN, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-dihydrouridine synthase B (EC 1.3.1.-) | protein | 306 | 47% helix, 17% strand | P0ABT7 |
| B | TRNA-dihydrouridine synthase B (EC 1.3.1.-) | protein | 306 | 44% helix, 17% strand | P0ABT7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.80 | 0.81 | 113 | FMN, GOL, SO4 |
| 2 | 361 | 0.74 | 0.85 | 49 | empty |
| 3 | 145 | 0.54 | 0.80 | 20 | empty |
| 4 | 76 | 0.29 | 0.73 | 21 | empty |
| 5 | 61 | 0.28 | 0.73 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 989 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6EI9 · Crystal structure of E. coli tRNA-dihydrouridine synthase B (DusB) · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABT7 · AlphaFold monomer V2.0 prediction for tRNA-dihydrouridine synthase B (P0ABT7) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0ABT7
- Elsewhere: RCSB PDB 6EI9 · PDBe 6EI9 · UniProt P0ABT7
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