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Crystal structure of escherichia COLI 23S rRNA (A2030-N6)- methyltransferase rlmj in complex with S-adenosylmethionine (adomet)
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
- 4BLV
- Type
- protein
- Length
- 556 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
- SAM, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 280 | 40% helix, 19% strand | P37634 |
| B | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 276 | 38% helix, 20% strand | P37634 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.74 | 0.85 | 47 | EDO, SO4 |
| 2 | 273 | 0.71 | 0.86 | 45 | SAM, EDO |
| 3 | 304 | 0.57 | 0.77 | 39 | SAM |
| 4 | 172 | 0.42 | 0.73 | 25 | GOL |
| 5 | 87 | 0.33 | 0.74 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4BLV · 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 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 P37634
- Elsewhere: RCSB PDB 4BLV · PDBe 4BLV · UniProt P37634
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