Research workbench
The structure of lepi complex with SAM and its substrate analogue
Analyse The structure of lepi complex with SAM and its substrate analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IX5
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase lepi
- EC
- 2.1.1.-
- UniProt
- B8NJH3
- Ligands
- SAM, B0L, NA, CL
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-methyltransferase lepi (EC 2.1.1.-) | protein | 389 | 53% helix, 13% strand | B8NJH3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- B0L · 4-hydroxy-3-[(2S,6E,8E)-2-methyldeca-6,8-dienoyl]-5-phenylpyridin-2(1H)-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.86 | 0.87 | 93 | SAM, B0L, EDO |
| 2 | 1174 | 0.85 | 0.86 | 98 | SAM, B0L, EDO, CL |
| 3 | 318 | 0.67 | 0.82 | 37 | CL |
| 4 | 128 | 0.58 | 0.84 | 20 | empty |
| 5 | 171 | 0.53 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 5086 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 6IX5 · The structure of LepI complex with SAM and its substrate analogue · the same entry in another collection · chain A against A, TM-score 1.00
- B8NJH3 · AlphaFold monomer V2.0 prediction for O-methyltransferase lepi (B8NJH3) · 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 B8NJH3
- Elsewhere: RCSB PDB 6IX5 · PDBe 6IX5 · UniProt B8NJH3
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