MolNFT v1 · #77448 · protein
X-ray structure of rlmn from escherichia COLI in complex with S- adenosylmethionine
3RFA · Ribosomal RNA large subunit methyltransferase N: “X-ray structure of rlmn from escherichia COLI in complex with S- adenosylmethionine”. X-ray diffraction, 2 ligands (SF4, SAM), 3 pockets (best druggability 0.84). MolNFT v1 #77448 on…
- PDB
- 3RFA
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase N
- EC
- 2.1.1.192
- UniProt
- P36979
- Ligands
- SF4, SAM
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase N (EC 2.1.1.192) | protein | 333 | 41% helix, 22% strand | P36979 |
| B | Ribosomal RNA large subunit methyltransferase N (EC 2.1.1.192) | protein | 359 | 41% helix, 20% strand | P36979 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.84 | 0.86 | 70 | SF4, SAM |
| 2 | 945 | 0.81 | 0.82 | 69 | SF4, SAM |
| 3 | 484 | 0.59 | 0.74 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 78 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3RFA · X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine · the same entry in another collection · chain B against B, TM-score 1.00
- P36979 · AlphaFold monomer V2.0 prediction for dual-specificity RNA methyltransferase rlmn (P36979) · a predicted model of the same protein · chain A 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 P36979
- Elsewhere: RCSB PDB 3RFA · PDBe 3RFA · UniProt P36979
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.