MolNFT v1 · #65497 · protein
Structure of the thiostrepton-resistance methyltransferase S-adenosyl-L-methionine complex
3GYQ · RRNA (adenosine-2'-O-)-methyltransferase: “Structure of the thiostrepton-resistance methyltransferase S-adenosyl-L-methionine complex”. X-ray diffraction, 1 ligand (SAM), 8 pockets (best druggability 0.78). MolNFT v1 #65497 on…
- PDB
- 3GYQ
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA (adenosine-2'-O-)-methyltransferase
- EC
- 2.1.1.66
- UniProt
- P18644
- Ligands
- SAM
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RRNA (adenosine-2'-O-)-methyltransferase (EC 2.1.1.66) | protein | 261 | 32% helix, 20% strand | P18644 |
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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.78 | 0.80 | 111 | SAM |
| 2 | 212 | 0.59 | 0.81 | 29 | empty |
| 3 | 152 | 0.53 | 0.80 | 23 | empty |
| 4 | 136 | 0.49 | 0.79 | 24 | empty |
| 5 | 68 | 0.49 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1310 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3GYQ · Structure of the Thiostrepton-Resistance Methyltransferase S-adenosyl-L-methionine Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P18644 · AlphaFold monomer V2.0 prediction for 23S rRNA (ADENOSINE(1067)-2'-O)-methyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P18644
- Elsewhere: RCSB PDB 3GYQ · PDBe 3GYQ · UniProt P18644
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