MolNFT v1 · #148182 · protein
Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase catalytic domain E294K mutant
6EZA · TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like: “Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase catalytic domain E294K mutant”. X-ray diffraction, 3 ligands (FMN, SO4, CL), 9 pockets (best druggability 0.62). MolNFT v1…
- PDB
- 6EZA
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- 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
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 317 | 48% helix, 19% strand | Q9NX74 |
| B | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 313 | 47% helix, 19% strand | Q9NX74 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.62 | 0.79 | 32 | FMN, CL |
| 2 | 257 | 0.61 | 0.80 | 30 | FMN, GOL |
| 3 | 429 | 0.56 | 0.74 | 42 | SO4, GOL |
| 4 | 141 | 0.53 | 0.81 | 21 | SO4 |
| 5 | 178 | 0.51 | 0.78 | 25 | SO4 |
Interfaces
1 interface between chains.
- A–B · 167 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EZA · Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K 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 B 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 6EZA · PDBe 6EZA · UniProt Q9NX74
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