MolNFT v1 · #86727 · protein
Crystal structure of E. COLI dihydrouridine synthase C (dusc)
4BFA · TRNA-dihydrouridine synthase C: “Crystal structure of E. COLI dihydrouridine synthase C (dusc)”. X-ray diffraction, 2 ligands (FMN, NO3), 6 pockets (best druggability 0.75). MolNFT v1 #86727 on GenesisL1: 3D structure, binding sites…
- PDB
- 4BFA
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-dihydrouridine synthase C
- EC
- 1.3.1.-
- UniProt
- P33371
- Ligands
- FMN, NO3
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-dihydrouridine synthase C (EC 1.3.1.-) | protein | 317 | 46% helix, 14% strand | P33371 |
| B | TRNA-dihydrouridine synthase C (EC 1.3.1.-) | protein | 307 | 47% helix, 16% strand | P33371 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.75 | 0.83 | 57 | EDO, NO3 |
| 2 | 289 | 0.62 | 0.80 | 50 | FMN |
| 3 | 219 | 0.62 | 0.82 | 35 | FMN |
| 4 | 88 | 0.33 | 0.74 | 18 | empty |
| 5 | 87 | 0.31 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4BFA · Crystal structure of E. coli dihydrouridine synthase C (DusC) · the same entry in another collection · chain A against A, TM-score 1.00
- P33371 · AlphaFold monomer V2.0 prediction for tRNA-DIHYDROURIDINE(16) synthase (P33371) · 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 P33371
- Elsewhere: RCSB PDB 4BFA · PDBe 4BFA · UniProt P33371
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