Research workbench
Structure of TRM8-TRM82, the yeast tRNA M7G methylation complex
Analyse Structure of TRM8-TRM82, the yeast tRNA M7G methylation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDU
- Type
- protein
- Length
- 1,152 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(7)-)-methyltransferase- associated wd repeat protein TRM82; TRNA…
- EC
- 2.1.1.33
- UniProt
- Q03774, Q12009
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA (guanine-N(7)-)-methyltransferase- associated wd repeat protein TRM82 | protein | 374 | 7% helix, 48% strand | Q03774 |
| D | TRNA (guanine-N(7)-)-methyltransferase- associated wd repeat protein TRM82 | protein | 376 | 7% helix, 48% strand | Q03774 |
| E, F | TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) | protein | 201 | 36% helix, 24% strand | Q12009 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.79 | 0.81 | 71 | empty |
| 2 | 1170 | 0.79 | 0.81 | 70 | empty |
| 3 | 353 | 0.57 | 0.76 | 45 | empty |
| 4 | 226 | 0.57 | 0.79 | 34 | empty |
| 5 | 327 | 0.56 | 0.76 | 45 | empty |
Interfaces
5 interfaces between chains.
- D–F · 1016 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 1004 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 922 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 85 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VDU · Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q03774 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(7)-)-methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q12009 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(7)-)-methyltransferase (Q12009) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 Q03774
- Every structure of UniProt Q12009
- Elsewhere: RCSB PDB 2VDU · PDBe 2VDU · UniProt Q03774 · UniProt Q12009
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