Research workbench
Crystal structure of human M1A58 methyltransferase in a complex with TRNA3LYS and sah
Analyse Crystal structure of human M1A58 methyltransferase in a complex with TRNA3LYS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CCB
- Type
- protein + RNA
- Length
- 730 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
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 33% 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 | 282 | 27% helix, 30% strand | Q96FX7 |
| B | TRNA (ADENINE(58)-N(1))-methyltransferase non-catalytic subunit TRM6 (EC 2.1.1.220) | protein | 371 | 38% 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
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.76 | 0.80 | 87 | empty |
| 2 | 722 | 0.68 | 0.77 | 54 | empty |
| 3 | 484 | 0.67 | 0.78 | 66 | empty |
| 4 | 453 | 0.61 | 0.76 | 46 | NA |
| 5 | 302 | 0.56 | 0.77 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2624 Ų buried · 31 hydrogen bonds · protein-protein
- B–N · 1752 Ų buried · 36 hydrogen bonds · protein-nucleic
Compared structures
- 5CCB · Crystal structure of human m1A58 methyltransferase in a complex with tRNA3Lys and SAH · 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 5CCB · PDBe 5CCB · UniProt Q96FX7 · UniProt Q9UJA5
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