MolNFT v1 · #153048 · protein
Crystal structure of a SAM-dependent methyltransferase lepi from aspergillus flavus
6J1O · O-methyltransferase lepi: “Crystal structure of a SAM-dependent methyltransferase lepi from aspergillus flavus”. X-ray diffraction, 2 ligands (SAM, MTA), 6 pockets (best druggability 0.86). MolNFT v1 #153048 on GenesisL1: 3D…
- PDB
- 6J1O
- Type
- protein
- Length
- 774 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, MTA
- 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 | 387 | 53% helix, 13% strand | B8NJH3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, 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 | 1155 | 0.86 | 0.86 | 95 | SAM, MTA |
| 2 | 1158 | 0.85 | 0.86 | 92 | SAM, MTA |
| 3 | 316 | 0.65 | 0.81 | 38 | empty |
| 4 | 258 | 0.63 | 0.82 | 38 | empty |
| 5 | 133 | 0.37 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4922 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6J1O · Crystal structure of a SAM-dependent methyltransferase LepI from Aspergillus flavus · 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 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 B8NJH3
- Elsewhere: RCSB PDB 6J1O · PDBe 6J1O · UniProt B8NJH3
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