Research workbench
The X-ray structure of yeast tRNA methyltransferase complex of TRM7 and TRM734 essential for 2'-O-methylation at the first position of anticodon in specific trnas
Analyse The X-ray structure of yeast tRNA methyltransferase complex of TRM7 and TRM734… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JP6
- Type
- protein
- Length
- 2,458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANOSINE(34)-2'-O)-methyltransferase non-catalytic subunit TRM734; TRNA…
- EC
- 2.1.1.205
- UniProt
- Q08924, P38238
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TRNA (GUANOSINE(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 | protein | 998 | 3% helix, 57% strand | Q08924 |
| B, D | TRNA (CYTIDINE(34)/GUANOSINE(34)-2'-O)-methyltransferase (EC 2.1.1.205) | protein | 231 | 35% helix, 23% strand | P38238 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.81 | 0.83 | 87 | empty |
| 2 | 942 | 0.81 | 0.83 | 93 | empty |
| 3 | 1042 | 0.80 | 0.82 | 93 | empty |
| 4 | 1077 | 0.80 | 0.82 | 100 | empty |
| 5 | 714 | 0.79 | 0.83 | 59 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1822 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1783 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1141 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 510 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6JP6 · The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08924 · AlphaFold monomer V2.0 prediction for regulator of TY1 transposition protein 10 (Q08924) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P38238 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE(32)/GUANOSINE(34)-2'-O)-methyltransfe… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q08924
- Every structure of UniProt P38238
- Elsewhere: RCSB PDB 6JP6 · PDBe 6JP6 · UniProt Q08924 · UniProt P38238
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