MolNFT v1 · #110969 · protein + RNA
E. COLI dihydrouridine synthase C (dusc) in complex with trnatrp
4YCP · TRNA-dihydrouridine synthase C: “E. COLI dihydrouridine synthase C (dusc) in complex with trnatrp”. X-ray diffraction, 3 ligands (FMN, MG, SO4), 4 pockets (best druggability 0.79). MolNFT v1 #110969 on GenesisL1: 3D structure…
- PDB
- 4YCP
- Type
- protein + RNA
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-dihydrouridine synthase C; Trnatrp
- EC
- 1.-.-.-
- UniProt
- P33371
- Ligands
- FMN, MG, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-dihydrouridine synthase C (EC 1.-.-.-) | protein | 308 | 48% helix, 13% strand | P33371 |
| B | Trnatrp | rna | 60 | — | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.79 | 0.82 | 64 | empty |
| 2 | 282 | 0.71 | 0.85 | 42 | FMN, MG |
| 3 | 645 | 0.64 | 0.75 | 39 | empty |
| 4 | 65 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 4YCP · E. coli dihydrouridine synthase C (DusC) in complex with tRNATrp · 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 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 P33371
- Elsewhere: RCSB PDB 4YCP · PDBe 4YCP · UniProt P33371
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