Research workbench
Structure of E.COLI rlmj in complex with an RNA conjugate (gaa-SAM)
Analyse Structure of E.COLI rlmj in complex with an RNA conjugate (gaa-SAM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P9I
- Type
- protein + RNA
- Length
- 550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase J; RNA conjugate (gaa-SAM)
- EC
- 2.1.1.266
- UniProt
- P37634
- Ligands
- 6D6
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 271 | 38% helix, 20% strand | P37634 |
| B | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 273 | 38% helix, 20% strand | P37634 |
| D, E | RNA conjugate (gaa-SAM) | rna | 3 | — | — |
Ligands and binding sites
- 6D6 · 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl) amino}-5'-deoxyadenosine · ligand · 2 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.75 | 0.88 | 39 | 6D6 |
| 2 | 268 | 0.73 | 0.87 | 39 | 6D6 |
| 3 | 339 | 0.60 | 0.77 | 42 | empty |
| 4 | 98 | 0.41 | 0.77 | 16 | empty |
| 5 | 97 | 0.39 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 437 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–E · 432 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 394 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 7P9I · Structure of E.coli RlmJ in complex with an RNA conjugate (GAA-SAM) · the same entry in another collection · chain D against D, 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 7P9I · PDBe 7P9I · UniProt P37634
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