Research workbench
T. thermophilus 16S rRNA G527 methyltransferase in complex with adomet and AMP in space group P61
Analyse T. thermophilus 16S rRNA G527 methyltransferase in complex with adomet and AMP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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