Research workbench
Crystal structure of tRNA-DIHYDROURIDINE(20) synthase dsrbd domain
Analyse Crystal structure of tRNA-DIHYDROURIDINE(20) synthase dsrbd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WFT
- Type
- protein
- Length
- 281 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like
- EC
- 1.3.1.-
- UniProt
- Q9NX74
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 94 | 34% helix, 27% strand | Q9NX74 |
| A | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 94 | 33% helix, 27% strand | Q9NX74 |
| B | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 93 | 34% helix, 27% strand | Q9NX74 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.56 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 544 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 474 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 85 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4WFT · Crystal structure of tRNA-dihydrouridine(20) synthase dsRBD domain · the same entry in another collection · chain C against C, TM-score 1.00
- Q9NX74 · AlphaFold monomer V2.0 prediction for tRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9NX74
- Elsewhere: RCSB PDB 4WFT · PDBe 4WFT · UniProt Q9NX74
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