Research workbench
Crystal structure of the two-subunit tRNA M1A58 methyltransferase TRM6-TRM61 in complex with SAM
Analyse Crystal structure of the two-subunit tRNA M1A58 methyltransferase TRM6-TRM61 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ERG
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (ADENINE(58)-N(1))-methyltransferase non-catalytic subunit TRM6; TRNA…
- EC
- 2.1.1.220
- UniProt
- P41814, P46959
- Ligands
- SAM
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (ADENINE(58)-N(1))-methyltransferase non-catalytic subunit TRM6 | protein | 340 | 33% helix, 26% strand | P41814 |
| B | TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit TRM61 (EC 2.1.1.220) | protein | 324 | 27% helix, 31% strand | P46959 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.77 | 0.82 | 66 | empty |
| 2 | 515 | 0.72 | 0.81 | 60 | empty |
| 3 | 217 | 0.51 | 0.76 | 40 | SAM |
| 4 | 72 | 0.33 | 0.75 | 13 | empty |
| 5 | 56 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3354 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 5ERG · Crystal structure of the two-subunit tRNA m1A58 methyltransferase TRM6-TRM61 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P41814 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.95
- P46959 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase catalytic… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P41814
- Every structure of UniProt P46959
- Elsewhere: RCSB PDB 5ERG · PDBe 5ERG · UniProt P41814 · UniProt P46959
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