MolNFT v1 · #58354 · protein + RNA
TRNA-dihydrouridine synthase from thermus thermophilus in complex with tRNA fragment
3B0U · RNA (5'-R(*GP*GP*(H2U)P*A)-3'): “TRNA-dihydrouridine synthase from thermus thermophilus in complex with tRNA fragment”. X-ray diffraction, 1 ligand (FMN), 7 pockets (best druggability 0.72). MolNFT v1 #58354 on GenesisL1: 3D…
- PDB
- 3B0U
- Type
- protein + RNA
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*GP*(H2U)P*A)-3'); TRNA-dihydrouridine synthase
- UniProt
- Q5SMC7
- Ligands
- FMN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*GP*GP*(H2U)P*A)-3') | rna | 4 | — | — |
| X, Y | TRNA-dihydrouridine synthase | protein | 312 | 49% helix, 15% strand | Q5SMC7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, X, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.72 | 0.87 | 37 | FMN |
| 2 | 208 | 0.70 | 0.87 | 31 | FMN |
| 3 | 361 | 0.59 | 0.77 | 30 | empty |
| 4 | 126 | 0.43 | 0.77 | 19 | empty |
| 5 | 90 | 0.40 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–Y · 694 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–X · 671 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–X · 105 Ų buried · 0 hydrogen bonds · protein-nucleic
- X–Y · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3B0U · tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA fragment · 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 X 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 Q5SMC7
- Elsewhere: RCSB PDB 3B0U · PDBe 3B0U · UniProt Q5SMC7
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