Research workbench
Crystal structure of archaeal tRNA-methylase for position 56 (ATRM56) from pyrococcus horikoshii, complexed with S- adenosyl-L-methionine
Analyse Crystal structure of archaeal tRNA-methylase for position 56 (ATRM56) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YY8
- Type
- protein
- Length
- 348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0106 protein PH0461
- UniProt
- O58214
- Ligands
- MTA, SAM
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0106 protein PH0461 | protein | 174 | 39% helix, 21% strand | O58214 |
| B | UPF0106 protein PH0461 | protein | 174 | 41% helix, 22% strand | O58214 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.69 | 0.84 | 34 | MTA |
| 2 | 285 | 0.65 | 0.82 | 33 | SAM |
| 3 | 56 | 0.43 | 0.83 | 16 | empty |
| 4 | 52 | 0.39 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2349 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2YY8 · Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O58214 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE(56)-2'-O)-methyltransferase (O58214) · 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 O58214
- Elsewhere: RCSB PDB 2YY8 · PDBe 2YY8 · UniProt O58214
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