Research workbench
Crystal structure of escherichia COLI 23S rRNA (A2030-N6)- methyltransferase rlmj in complex with S-adenosylhomocysteine (adohcy) and adenosine monophosphate (AMP)
Analyse Crystal structure of escherichia COLI 23S rRNA (A2030-N6)- methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BLW
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase J
- EC
- 2.1.1.266
- UniProt
- P37634
- Ligands
- AMP, SAH, NA, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 280 | 39% helix, 19% strand | P37634 |
| B | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 279 | 40% helix, 19% strand | P37634 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.70 | 0.81 | 55 | EDO, SO4 |
| 2 | 336 | 0.70 | 0.83 | 60 | AMP, SAH, EDO, NA |
| 3 | 345 | 0.69 | 0.82 | 48 | AMP, SAH, EDO, NA |
| 4 | 229 | 0.46 | 0.73 | 33 | EDO |
| 5 | 88 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4BLW · Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in… · the same entry in another collection · chain A against A, TM-score 1.00
- P37634 · AlphaFold monomer V2.0 prediction for ribosomal RNA large subunit methyltransferase J… · 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 P37634
- Elsewhere: RCSB PDB 4BLW · PDBe 4BLW · UniProt P37634
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