Research workbench
Crystal structure of human tRNA dihydrouridine synthase 2
Analyse Crystal structure of human tRNA dihydrouridine synthase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XP7
- Type
- protein
- Length
- 324 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
- FNR
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-) | protein | 324 | 46% helix, 18% strand | Q9NX74 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.51 | 0.76 | 36 | FNR |
| 2 | 141 | 0.50 | 0.79 | 24 | empty |
| 3 | 68 | 0.32 | 0.75 | 13 | empty |
| 4 | 59 | 0.29 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4XP7 · Crystal structure of Human tRNA dihydrouridine synthase 2 · 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 4XP7 · PDBe 4XP7 · UniProt Q9NX74
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