MolNFT v1 · #115214 · protein + RNA
Structure of the product complex of tRNA M1A58 methyltransferase with TRNA3LYS as substrate
5CCX · TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit…: “Structure of the product complex of tRNA M1A58 methyltransferase with TRNA3LYS as substrate”. X-ray diffraction, 2 ligands (SAH, NA), 9 pockets (best druggability 0.76).…
- PDB
- 5CCX
- Type
- protein + RNA
- Length
- 731 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit TRMT61A; TRNA…
- EC
- 2.1.1.220
- UniProt
- Q96FX7, Q9UJA5
- Ligands
- SAH, NA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit TRMT61A (EC 2.1.1.220) | protein | 283 | 27% helix, 30% strand | Q96FX7 |
| B | TRNA (ADENINE(58)-N(1))-methyltransferase non-catalytic subunit TRM6 | protein | 371 | 36% helix, 24% strand | Q9UJA5 |
| N | TRNA3LYS | rna | 77 | — | — |
Ligands and binding sites
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 | 841 | 0.76 | 0.80 | 84 | empty |
| 2 | 515 | 0.68 | 0.79 | 54 | empty |
| 3 | 475 | 0.66 | 0.78 | 67 | empty |
| 4 | 371 | 0.63 | 0.78 | 38 | empty |
| 5 | 181 | 0.55 | 0.80 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2580 Ų buried · 30 hydrogen bonds · protein-protein
- B–N · 1768 Ų buried · 35 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5CCX · Structure of the product complex of tRNA m1A58 methyltransferase with tRNA3Lys as… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96FX7 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase catalytic… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9UJA5 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q96FX7
- Every structure of UniProt Q9UJA5
- Elsewhere: RCSB PDB 5CCX · PDBe 5CCX · UniProt Q96FX7 · UniProt Q9UJA5
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