MolNFT v1 · #52139 · protein
The crystal structure of pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine
2VS1 · Uncharacterized RNA methyltransferase PYRAB10780: “The crystal structure of pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with…”. X-ray diffraction, 2 ligands (SAH, PO4), 3 pockets (best druggability 0.57).…
- PDB
- 2VS1
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized RNA methyltransferase PYRAB10780
- EC
- 2.1.1.-
- UniProt
- Q9UZR7
- Ligands
- SAH, PO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized RNA methyltransferase PYRAB10780 (EC 2.1.1.-) | protein | 398 | 23% helix, 34% strand | Q9UZR7 |
Ligands and binding sites
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 | 307 | 0.57 | 0.77 | 34 | SAH |
| 2 | 163 | 0.48 | 0.77 | 25 | empty |
| 3 | 60 | 0.42 | 0.82 | 20 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, oxidation).
Compared structures
- 2VS1 · The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UZR7 · AlphaFold monomer V2.0 prediction for tRNA (URACIL(54)-C(5))-methyltransferase (Q9UZR7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9UZR7
- Elsewhere: RCSB PDB 2VS1 · PDBe 2VS1 · UniProt Q9UZR7
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