Research workbench
Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA M6A1832 methyltransferase at 2.5A resolution
Analyse Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA M6A1832… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H2V
- Type
- protein
- Length
- 630 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase-like protein 5; Multifunctional methyltransferase subunit TRM112-like…
- EC
- 2.1.1.-
- UniProt
- Q9NRN9, Q9UI30
- Ligands
- SAM, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase-like protein 5 (EC 2.1.1.-) | protein | 210 | 34% helix, 26% strand | Q9NRN9 |
| B | Multifunctional methyltransferase subunit TRM112-like protein | protein | 111 | 37% helix, 23% strand | Q9UI30 |
| C | Methyltransferase-like protein 5 (EC 2.1.1.-) | protein | 194 | 37% helix, 27% strand | Q9NRN9 |
| D | Multifunctional methyltransferase subunit TRM112-like protein | protein | 115 | 38% helix, 23% strand | Q9UI30 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, D
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.78 | 0.82 | 86 | empty |
| 2 | 287 | 0.70 | 0.84 | 41 | SAM, PG0 |
| 3 | 129 | 0.65 | 0.87 | 30 | SAM |
| 4 | 122 | 0.64 | 0.88 | 17 | EDO, PG0 |
| 5 | 143 | 0.57 | 0.82 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1187 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1175 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1008 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 6H2V · Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NRN9 · AlphaFold monomer V2.0 prediction for rRNA N6-adenosine- methyltransferase METTL5 (Q9NRN9) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q9UI30 · AlphaFold monomer V2.0 prediction for multifunctional methyltransferase subunit… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9NRN9
- Every structure of UniProt Q9UI30
- Elsewhere: RCSB PDB 6H2V · PDBe 6H2V · UniProt Q9NRN9 · UniProt Q9UI30
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