Research workbench
Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase catalytic domain E294K Q305K double 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
- 6EZC
- Type
- protein
- Length
- 308 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, CL
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 308 | 48% helix, 18% strand | Q9NX74 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PGE · Triethylene glycol · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.48 | 0.79 | 19 | SO4, PGE |
| 2 | 189 | 0.48 | 0.76 | 28 | FMN, CL, GOL |
| 3 | 90 | 0.40 | 0.77 | 19 | empty |
Compared structures
- 6EZC · Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K… · 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 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 Q9NX74
- Elsewhere: RCSB PDB 6EZC · PDBe 6EZC · UniProt Q9NX74
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