Research workbench
Crystal structure of the spou methyltransferase avirb from streptomyces viridochromogenes in complex with the cofactor adomet
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
- 1X7P
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q9F5K6
- Ligands
- SAM
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA methyltransferase (EC 2.1.1.-) | protein | 265 | 37% helix, 21% strand | Q9F5K6 |
| B | RRNA methyltransferase (EC 2.1.1.-) | protein | 253 | 40% helix, 19% strand | Q9F5K6 |
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
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 | 692 | 0.73 | 0.80 | 71 | SAM |
| 2 | 59 | 0.56 | 0.88 | 14 | empty |
| 3 | 113 | 0.43 | 0.77 | 22 | empty |
| 4 | 59 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1288 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1X7P · 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 0.98
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 1X7P · PDBe 1X7P · UniProt Q9F5K6
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