Research workbench
T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (ksga) in complex with 5'-methylthioadenosine in space group P212121
Analyse T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (ksga) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FUX
- Type
- protein
- Length
- 793 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethyladenosine transferase
- EC
- 2.1.1.-
- UniProt
- Q5SM60
- Ligands
- MTA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dimethyladenosine transferase (EC 2.1.1.-) | protein | 264 | 46% helix, 19% strand | Q5SM60 |
| C | Dimethyladenosine transferase (EC 2.1.1.-) | protein | 265 | 46% helix, 18% strand | Q5SM60 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 3 copies · chains A, B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.82 | 0.83 | 120 | MTA |
| 2 | 193 | 0.74 | 0.90 | 46 | MTA |
| 3 | 269 | 0.73 | 0.86 | 54 | MTA |
| 4 | 392 | 0.70 | 0.82 | 36 | empty |
| 5 | 277 | 0.49 | 0.73 | 33 | empty |
Interfaces
3 interfaces between chains.
- B–C · 731 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 390 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 142 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FUX · T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SM60 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase a… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5SM60
- Elsewhere: RCSB PDB 3FUX · PDBe 3FUX · UniProt Q5SM60
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