Research workbench
Pyrococcus abyssi methyltransferase PATRM5A bound by mta and cognate tRNA
Analyse Pyrococcus abyssi methyltransferase PATRM5A bound by mta and cognate tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WT3
- Type
- protein + RNA
- Length
- 405 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANINE(37)-N1)-methyltransferase TRM5A; RNA (73-mer)
- EC
- 2.1.1.228
- UniProt
- Q9V2G1
- Ligands
- MTA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (GUANINE(37)-N1)-methyltransferase TRM5A (EC 2.1.1.228) | protein | 332 | 33% helix, 32% strand | Q9V2G1 |
| C | RNA (73-mer) | rna | 73 | — | — |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.78 | 0.83 | 49 | empty |
| 2 | 175 | 0.74 | 0.90 | 30 | MTA |
| 3 | 741 | 0.66 | 0.75 | 31 | empty |
| 4 | 235 | 0.65 | 0.83 | 35 | empty |
| 5 | 77 | 0.61 | 0.89 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 2276 Ų buried · 56 hydrogen bonds · protein-nucleic
Compared structures
- 5WT3 · Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V2G1 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(37)-N1)/4-DEMETHYLWYOSINE(37)-methyltr… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9V2G1
- Elsewhere: RCSB PDB 5WT3 · PDBe 5WT3 · UniProt Q9V2G1
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