Research workbench
Pyrococcus abyssi methyltransferase PATRM5A bound by sah and cognate tRNA
Analyse Pyrococcus abyssi methyltransferase PATRM5A bound by sah 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
- 5WT1
- Type
- protein + RNA
- Length
- 797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANINE(37)-N1)-methyltransferase TRM5A; RNA (76-mer)
- EC
- 2.1.1.228
- UniProt
- Q9V2G1
- Ligands
- SAH
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (GUANINE(37)-N1)-methyltransferase TRM5A (EC 2.1.1.228) | protein | 332 | 34% helix, 34% strand | Q9V2G1 |
| C | RNA (76-mer) | rna | 67 | — | — |
| B | TRNA (GUANINE(37)-N1)-methyltransferase TRM5A (EC 2.1.1.228) | protein | 330 | 33% helix, 33% strand | Q9V2G1 |
| F | RNA (76-mer) | rna | 68 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.77 | 0.82 | 44 | empty |
| 2 | 738 | 0.76 | 0.82 | 42 | empty |
| 3 | 55 | 0.72 | 0.99 | 20 | empty |
| 4 | 164 | 0.72 | 0.89 | 33 | SAH |
| 5 | 152 | 0.68 | 0.88 | 33 | SAH |
Interfaces
2 interfaces between chains.
- A–C · 2466 Ų buried · 57 hydrogen bonds · protein-nucleic
- B–F · 2331 Ų buried · 47 hydrogen bonds · protein-nucleic
Compared structures
- 5WT1 · Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH 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 B against A, TM-score 0.95
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 5WT1 · PDBe 5WT1 · UniProt Q9V2G1
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