Research workbench
Structure of E.COLI rlmj in complex with an RNA conjugate (ga-SAM)
Analyse Structure of E.COLI rlmj in complex with an RNA conjugate (ga-SAM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P8Q
- Type
- protein + RNA
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase J; RNA conjugate (ga-SAM)
- EC
- 2.1.1.266
- UniProt
- P37634
- Ligands
- 6D6
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 275 | 37% helix, 20% strand | P37634 |
| B | RNA conjugate (ga-SAM) | rna | 2 | — | — |
Ligands and binding sites
- 6D6 · 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl) amino}-5'-deoxyadenosine · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.57 | 0.78 | 37 | 6D6 |
| 2 | 87 | 0.35 | 0.74 | 17 | empty |
| 3 | 69 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 416 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 7P8Q · Structure of E.coli RlmJ in complex with an RNA conjugate (GA-SAM) · 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 0.98
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 P37634
- Elsewhere: RCSB PDB 7P8Q · PDBe 7P8Q · UniProt P37634
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