Research workbench
The structure of lepi C52A in complex with SAM and its substrate analogue
Analyse The structure of lepi C52A in 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
- 6IX8
- 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, B3O, NA, CL
- Pockets
- 6 · 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
- B3O · (1r,2r,4as,8s,8ar)-2,8-dimethyl-5'-phenyl-4A,5,6,7,8, 8A-hexahydro-2H,2'H-spiro[naphthalene-1,3'-pyridine]-2',4'(1'H)-dione · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.86 | 0.86 | 90 | SAM, B3O |
| 2 | 1150 | 0.85 | 0.86 | 92 | SAM, B3O |
| 3 | 318 | 0.65 | 0.81 | 39 | CL, NA, EDO |
| 4 | 243 | 0.62 | 0.82 | 36 | empty |
| 5 | 132 | 0.36 | 0.72 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 5069 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6IX8 · The structure of LepI C52A in 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 6IX8 · PDBe 6IX8 · UniProt B8NJH3
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