MolNFT v1 · #86040 · protein
Crystal structure of C2498 2'-O-ribose methyltransferase rlmm from escherichia COLI
4AUK · Ribosomal RNA large subunit methyltransferase M: “Crystal structure of C2498 2'-O-ribose methyltransferase rlmm from escherichia COLI”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.50). MolNFT v1 #86040 on…
- PDB
- 4AUK
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- 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
- SO4
- Pockets
- 9 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 34% 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 |
| B | Ribosomal RNA large subunit methyltransferase M (EC 2.1.1.186) | protein | 355 | 34% helix, 23% strand | P0ADR6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.50 | 0.79 | 32 | EDO |
| 2 | 103 | 0.45 | 0.79 | 22 | EDO |
| 3 | 56 | 0.45 | 0.84 | 15 | TRS |
| 4 | 97 | 0.45 | 0.80 | 26 | empty |
| 5 | 134 | 0.42 | 0.75 | 22 | GOL, PGE, EDO |
Interfaces
1 interface between chains.
- A–B · 884 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 4AUK · Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli · 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 B against A, TM-score 1.00
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 4AUK · PDBe 4AUK · UniProt P0ADR6
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