MolNFT v1 · #64604 · protein
T. thermophilus 16S rRNA G527 methyltransferase in complex with adomet and AMP in space group P61
3G89 · Ribosomal RNA small subunit methyltransferase G: “T. thermophilus 16S rRNA G527 methyltransferase in complex with adomet and AMP in space group P61”. X-ray diffraction, 2 ligands (SAM, AMP), 5 pockets (best druggability 0.57).…
- PDB
- 3G89
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- 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
- SAM, AMP
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 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 | 239 | 41% helix, 22% strand | Q9LCY2 |
| B | Ribosomal RNA small subunit methyltransferase G (EC 2.1.1.-) | protein | 238 | 41% helix, 22% strand | Q9LCY2 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.57 | 0.80 | 32 | empty |
| 2 | 173 | 0.55 | 0.80 | 33 | empty |
| 3 | 143 | 0.43 | 0.75 | 25 | empty |
| 4 | 81 | 0.41 | 0.78 | 16 | SAM |
| 5 | 97 | 0.38 | 0.75 | 20 | SAM |
Interfaces
1 interface between chains.
- A–B · 755 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, methylation).
Compared structures
- 3G89 · T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoMet and AMP in space… · the same entry in another collection · chain B against B, 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 B 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 3G89 · PDBe 3G89 · UniProt Q9LCY2
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