Research workbench
Multi-site-specific 16S rRNA methyltransferase rsmf from thermus thermophilus in space group P2 in complex with S-adenosyl-L- methionine
Analyse Multi-site-specific 16S rRNA methyltransferase rsmf from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M6V
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA methylase
- EC
- 2.1.1.-
- UniProt
- Q5SII2
- Ligands
- SAM
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RRNA methylase (EC 2.1.1.-) | protein | 458 | 32% helix, 26% strand | Q5SII2 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.74 | 0.77 | 100 | SAM |
| 2 | 334 | 0.56 | 0.75 | 49 | SAM |
| 3 | 61 | 0.35 | 0.78 | 19 | empty |
| 4 | 54 | 0.34 | 0.79 | 15 | empty |
| 5 | 58 | 0.33 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 365 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3M6V · Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SII2 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase F… · 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 Q5SII2
- Elsewhere: RCSB PDB 3M6V · PDBe 3M6V · UniProt Q5SII2
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