Research workbench
Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase catalytic domain Q305K mutant
Analyse Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase catalytic domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EZB
- Type
- protein
- Length
- 312 residues
- Chains
- 1
- 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
- Ligands
- FMN, SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 312 | 45% helix, 19% strand | Q9NX74 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.56 | 0.78 | 32 | FMN, GOL, SO4 |
| 2 | 124 | 0.45 | 0.78 | 18 | SO4 |
| 3 | 92 | 0.39 | 0.76 | 19 | empty |
Compared structures
- 6EZB · Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain Q305K mutant · the same entry in another collection · chain A against A, 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 0.99
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 Q9NX74
- Elsewhere: RCSB PDB 6EZB · PDBe 6EZB · UniProt Q9NX74
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