MolNFT v1 · #27037 · protein
Crystal structure of the spou methyltransferase avirb from streptomyces viridochromogenes in complex with the cofactor adomet
1X7P · RRNA methyltransferase: “Crystal structure of the spou methyltransferase avirb from streptomyces viridochromogenes in complex with the…”. X-ray diffraction, 1 ligand (SAM), 4 pockets (best druggability 0.73). MolNFT v1 #27037 on…
- 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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