Research workbench
E. COLI dihydrouridine synthase C (dusc) in complex with trnaphe
Analyse E. COLI dihydrouridine synthase C (dusc) in complex with trnaphe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YCO
- Type
- protein + RNA
- Length
- 1,143 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-dihydrouridine synthase C; Trnaphe
- EC
- 1.-.-.-
- UniProt
- P33371
- Ligands
- FMN, MG, MN
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TRNA-dihydrouridine synthase C (EC 1.-.-.-) | protein | 311 | 46% helix, 14% strand | P33371 |
| B | TRNA-dihydrouridine synthase C (EC 1.-.-.-) | protein | 309 | 47% helix, 14% strand | P33371 |
| D | Trnaphe | rna | 74 | — | — |
| E | Trnaphe | rna | 67 | — | — |
| F | Trnaphe | rna | 71 | — | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 3 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 25 copies · chains B, E, D, A, F, C
- MN · Manganese (II) ion · metal · 3 copies · chains D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.85 | 0.87 | 83 | FMN, MG |
| 2 | 981 | 0.83 | 0.84 | 85 | MG, FMN |
| 3 | 1182 | 0.79 | 0.81 | 75 | MG |
| 4 | 280 | 0.73 | 0.86 | 45 | FMN |
| 5 | 887 | 0.69 | 0.76 | 55 | MN, MG |
Interfaces
7 interfaces between chains.
- A–D · 1111 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–F · 1097 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–E · 1078 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 672 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YCO · E. coli dihydrouridine synthase C (DusC) in complex with tRNAPhe · the same entry in another collection · chain F against F, TM-score 1.00
- P33371 · AlphaFold monomer V2.0 prediction for tRNA-DIHYDROURIDINE(16) synthase (P33371) · a predicted model of the same protein · chain C 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 4YCO · PDBe 4YCO · UniProt P33371
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