Research workbench
Structure of an antibiotic related methyltransferase
Analyse Structure of an antibiotic related methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P2K
- Type
- protein
- Length
- 788 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA methylase
- UniProt
- A8C927
- Ligands
- SAM
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 16S rRNA methylase | protein | 197 | 39% helix, 28% strand | A8C927 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.71 | 0.86 | 36 | SAM |
| 2 | 253 | 0.69 | 0.85 | 39 | SAM |
| 3 | 177 | 0.58 | 0.81 | 27 | SAM |
| 4 | 198 | 0.56 | 0.80 | 28 | SAM |
| 5 | 65 | 0.40 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–D · 510 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3P2K · Structure of an antibiotic related Methyltransferase · the same entry in another collection · chain D against D, TM-score 1.00
- A8C927 · AlphaFold monomer V2.0 prediction for 16S rRNA (ADENINE(1408)-N(1))-methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A8C927
- Elsewhere: RCSB PDB 3P2K · PDBe 3P2K · UniProt A8C927
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