Research workbench
Crystal structure of a radical SAM methyltransferase from sphaerobacter thermophilus
Analyse Crystal structure of a radical SAM methyltransferase from sphaerobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FZ6
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable dual-specificity RNA methyltransferase rlmn
- EC
- 2.1.1.192
- UniProt
- D1C4T7
- Ligands
- SF4, SAH, BR
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable dual-specificity RNA methyltransferase rlmn (EC 2.1.1.192) | protein | 341 | 41% helix, 19% strand | D1C4T7 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.82 | 0.95 | 31 | SF4, SAH |
| 2 | 590 | 0.80 | 0.85 | 65 | SF4, SAH |
| 3 | 327 | 0.65 | 0.80 | 33 | empty |
| 4 | 92 | 0.48 | 0.81 | 24 | empty |
| 5 | 159 | 0.46 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 341 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6FZ6 · Crystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
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 D1C4T7
- Elsewhere: RCSB PDB 6FZ6 · PDBe 6FZ6 · UniProt D1C4T7
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