Research workbench
TRNA-dihydrouridine synthase from thermus thermophilus
Analyse TRNA-dihydrouridine synthase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B0P
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-dihydrouridine synthase
- UniProt
- Q5SMC7
- Ligands
- FMN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-dihydrouridine synthase | protein | 307 | 50% helix, 14% strand | Q5SMC7 |
| B | TRNA-dihydrouridine synthase | protein | 308 | 51% helix, 14% strand | Q5SMC7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.77 | 0.79 | 97 | FMN |
| 2 | 383 | 0.58 | 0.75 | 39 | empty |
| 3 | 121 | 0.39 | 0.75 | 24 | empty |
| 4 | 82 | 0.39 | 0.77 | 19 | empty |
| 5 | 110 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 499 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3B0P · tRNA-dihydrouridine synthase from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SMC7 · AlphaFold monomer V2.0 prediction for tRNA-DIHYDROURIDINE(20/20A) synthase (Q5SMC7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5SMC7
- Elsewhere: RCSB PDB 3B0P · PDBe 3B0P · UniProt Q5SMC7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.