Research workbench
Crystal structure of the spou methyltransferase avirb from streptomyces viridochromogenes
Analyse Crystal structure of the spou methyltransferase avirb from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X7O
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q9F5K6
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA methyltransferase (EC 2.1.1.-) | protein | 267 | 38% helix, 21% strand | Q9F5K6 |
| B | RRNA methyltransferase (EC 2.1.1.-) | protein | 257 | 41% helix, 21% strand | Q9F5K6 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.69 | 0.77 | 55 | empty |
| 2 | 186 | 0.65 | 0.85 | 24 | empty |
| 3 | 98 | 0.43 | 0.78 | 20 | empty |
| 4 | 53 | 0.34 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1416 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1X7O · Crystal structure of the SpoU Methyltransferase AviRb from Streptomyces viridochromogenes · the same entry in another collection · chain A against A, TM-score 1.00
- Q9F5K6 · AlphaFold monomer V2.0 prediction for 23S rRNA (URIDINE(2479)-2'-O)-methyltransferase… · 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 Q9F5K6
- Elsewhere: RCSB PDB 1X7O · PDBe 1X7O · UniProt Q9F5K6
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