Research workbench
Structure of the product complex of tRNA M1A58 methyltransferase with TRNA3LYS as substrate
Analyse Structure of the product complex of tRNA M1A58 methyltransferase with TRNA3LYS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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