MolNFT v1 · #72835 · protein
Structure of the nosiheptide-resistance methyltransferase S-adenosyl- L-methionine complex
3NK7 · 23S rRNA methyltransferase: “Structure of the nosiheptide-resistance methyltransferase S-adenosyl- L-methionine complex”. X-ray diffraction, 1 ligand (SAM), 4 pockets (best druggability 0.74). MolNFT v1 #72835 on GenesisL1: 3D…
- PDB
- 3NK7
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA methyltransferase
- EC
- 2.1.1.-
- UniProt
- P52391
- Ligands
- SAM
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA methyltransferase (EC 2.1.1.-) | protein | 265 | 39% helix, 20% strand | P52391 |
| B | 23S rRNA methyltransferase (EC 2.1.1.-) | protein | 267 | 38% helix, 20% strand | P52391 |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.74 | 0.81 | 90 | SAM |
| 2 | 86 | 0.36 | 0.75 | 22 | empty |
| 3 | 83 | 0.36 | 0.76 | 19 | empty |
| 4 | 83 | 0.34 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1329 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3NK7 · Structure of the Nosiheptide-resistance methyltransferase S-adenosyl-L-methionine Complex · the same entry in another collection · chain B against B, TM-score 1.00
- P52391 · AlphaFold monomer V2.0 prediction for 23S rRNA (ADENOSINE(1067)-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 P52391
- Elsewhere: RCSB PDB 3NK7 · PDBe 3NK7 · UniProt P52391
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