MolNFT v1 · #152904 · protein
The structure of lepi C52A in complex with SAM and its substrate analogue
6IX8 · O-methyltransferase lepi: “The structure of lepi C52A in complex with SAM and its substrate analogue”. X-ray diffraction, 4 ligands (SAM, B3O, NA), 6 pockets (best druggability 0.86). MolNFT v1 #152904 on GenesisL1: 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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