Research workbench
Structure of E.COLI rlmj in complex with the natural cofactor product S-adenosyl-homocysteine (sah)
Analyse Structure of E.COLI rlmj in complex with the natural cofactor product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QE5
- Type
- protein
- Length
- 543 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
- A0A0G3KF30
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.72
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 | 270 | 39% helix, 20% strand | A0A0G3KF30 |
| B | Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266) | protein | 273 | 39% helix, 20% strand | A0A0G3KF30 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.72 | 0.86 | 45 | SAH |
| 2 | 365 | 0.71 | 0.83 | 56 | SAH |
| 3 | 87 | 0.54 | 0.85 | 19 | empty |
| 4 | 79 | 0.33 | 0.74 | 17 | empty |
| 5 | 65 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 699 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6QE5 · Structure of E.coli RlmJ in complex with the natural cofactor product… · the same entry in another collection · chain A 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 A0A0G3KF30
- Elsewhere: RCSB PDB 6QE5 · PDBe 6QE5 · UniProt A0A0G3KF30
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