MolNFT v1 · #64605 · protein
T. thermophilus 16S rRNA G527 methyltransferase in complex with adohcy in space group P61
3G8A · Ribosomal RNA small subunit methyltransferase G: “T. thermophilus 16S rRNA G527 methyltransferase in complex with adohcy in space group P61”. X-ray diffraction, 1 ligand (SAH), 17 pockets (best druggability 0.77). MolNFT v1 #64605…
- PDB
- 3G8A
- Type
- protein
- Length
- 1,430 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA small subunit methyltransferase G
- EC
- 2.1.1.-
- UniProt
- Q9LCY2
- Ligands
- SAH
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA small subunit methyltransferase G (EC 2.1.1.-) | protein | 236 | 41% helix, 22% strand | Q9LCY2 |
| B, D, E, F | Ribosomal RNA small subunit methyltransferase G (EC 2.1.1.-) | protein | 239 | 41% helix, 22% strand | Q9LCY2 |
| C | Ribosomal RNA small subunit methyltransferase G (EC 2.1.1.-) | protein | 238 | 40% helix, 22% strand | Q9LCY2 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.77 | 0.80 | 78 | empty |
| 2 | 818 | 0.73 | 0.78 | 63 | empty |
| 3 | 191 | 0.59 | 0.81 | 29 | empty |
| 4 | 149 | 0.51 | 0.79 | 31 | empty |
| 5 | 182 | 0.49 | 0.77 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–B · 733 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 728 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 457 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 451 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 451 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 modified (disulfide, methylation).
Compared structures
- 3G8A · T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoHcy in space group P61 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9LCY2 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase G… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9LCY2
- Elsewhere: RCSB PDB 3G8A · PDBe 3G8A · UniProt Q9LCY2
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