MolNFT v1 · #86262 · protein
Crystal structure of C2498 2'-O-ribose methyltransferase rlmm from escherichia COLI in complex with S-adenosylmethionine
4B17 · Ribosomal RNA large subunit methyltransferase M: “Crystal structure of C2498 2'-O-ribose methyltransferase rlmm from escherichia COLI in complex with…”. X-ray diffraction, 2 ligands (SAM, SO4), 3 pockets (best druggability 0.45).…
- PDB
- 4B17
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase M
- EC
- 2.1.1.186
- UniProt
- P0ADR6
- Ligands
- SAM, SO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase M (EC 2.1.1.186) | protein | 357 | 33% helix, 23% strand | P0ADR6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.45 | 0.77 | 24 | empty |
| 2 | 96 | 0.36 | 0.75 | 13 | EDO |
| 3 | 58 | 0.29 | 0.74 | 12 | EDO |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4B17 · Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli in… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ADR6 · AlphaFold monomer V2.0 prediction for ribosomal RNA large subunit methyltransferase M… · a predicted model of the same protein · chain A 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 P0ADR6
- Elsewhere: RCSB PDB 4B17 · PDBe 4B17 · UniProt P0ADR6
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