Research workbench
Structure of S. cerevisiae BUD23-TRM112 complex involved in formation of M7G1575 on 18S rRNA (SAM bound form)
Analyse Structure of S. cerevisiae BUD23-TRM112 complex involved in formation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QTU
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional methyltransferase subunit TRM112; Putative methyltransferase BUD23
- EC
- 2.1.1.-
- UniProt
- P53738, P25627
- Ligands
- SAM, ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multifunctional methyltransferase subunit TRM112 | protein | 134 | 34% helix, 19% strand | P53738 |
| B | Putative methyltransferase BUD23 (EC 2.1.1.-) | protein | 191 | 42% helix, 25% strand | P25627 |
| C | Multifunctional methyltransferase subunit TRM112 | protein | 135 | 32% helix, 19% strand | P53738 |
| D | Putative methyltransferase BUD23 (EC 2.1.1.-) | protein | 179 | 42% helix, 27% strand | P25627 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, D
- ZN · Zinc ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.71 | 0.85 | 41 | SAM, EDO |
| 2 | 160 | 0.56 | 0.80 | 19 | empty |
| 3 | 190 | 0.55 | 0.79 | 29 | SAM |
| 4 | 305 | 0.53 | 0.75 | 37 | EDO |
| 5 | 178 | 0.53 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1288 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1275 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 555 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4QTU · Structure of S. cerevisiae Bud23-Trm112 complex involved in formation of m7G1575 on 18S… · the same entry in another collection · chain A against A, TM-score 1.00
- P25627 · AlphaFold monomer V2.0 prediction for 18S rRNA (GUANINE(1575)-N(7))-methyltransferase… · a predicted model of the same protein · chain D against A, TM-score 0.99
- P53738 · AlphaFold monomer V2.0 prediction for multifunctional methyltransferase subunit TRM112… · a predicted model of the same protein · chain A 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 P53738
- Every structure of UniProt P25627
- Elsewhere: RCSB PDB 4QTU · PDBe 4QTU · UniProt P53738 · UniProt P25627
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