Research workbench
Multi-site-specific 16S rRNA methyltransferase rsmf from thermus thermophilus in space group 43
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
- 3M6U
- Type
- protein
- Length
- 873 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
- SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA methylase (EC 2.1.1.-) | protein | 438 | 30% helix, 28% strand | Q5SII2 |
| B | RRNA methylase (EC 2.1.1.-) | protein | 435 | 30% helix, 29% strand | Q5SII2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.75 | 0.78 | 111 | SO4 |
| 2 | 108 | 0.38 | 0.75 | 19 | empty |
| 3 | 73 | 0.36 | 0.77 | 16 | empty |
| 4 | 78 | 0.30 | 0.73 | 18 | empty |
| 5 | 57 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3M6U · Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space… · the same entry in another collection · chain B against B, 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 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 Q5SII2
- Elsewhere: RCSB PDB 3M6U · PDBe 3M6U · UniProt Q5SII2
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