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The X-ray structure of yeast tRNA methyltransferase TRM7-TRM734 in complex with S-adenosyl-L-methionine
Analyse The X-ray structure of yeast tRNA methyltransferase TRM7-TRM734 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JPL
- 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
- SAM, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 51% 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
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 10 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 | 1028 | 0.82 | 0.83 | 101 | empty |
| 2 | 1033 | 0.81 | 0.82 | 89 | empty |
| 3 | 954 | 0.81 | 0.82 | 93 | empty |
| 4 | 1027 | 0.79 | 0.81 | 125 | SAM |
| 5 | 1032 | 0.79 | 0.81 | 126 | SAM |
Interfaces
6 interfaces between chains.
- C–D · 1802 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1785 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1202 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 500 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6JPL · The X-ray structure of yeast tRNA methyltransferase Trm7-Trm734 in complex with… · the same entry in another collection · chain B against B, 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 C 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 6JPL · PDBe 6JPL · UniProt Q08924 · UniProt P38238
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