MolNFT v1 · #152088 · protein
Structure of fragaria ananassa O-methyltransferase in complex with S- adenosylhomocysteine and protocatechuic aldehyde
6I73: “Structure of fragaria ananassa O-methyltransferase in complex with S- adenosylhomocysteine and protocatechuic…”. X-ray diffraction, 3 ligands (SAH, H6N, SO4), 11 pockets (best druggability 0.84). MolNFT v1 #152088 on GenesisL1: 3D…
- PDB
- 6I73
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase
- UniProt
- Q9M602
- Ligands
- SAH, H6N, SO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-methyltransferase | protein | 353 | 48% helix, 17% strand | Q9M602 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- H6N · Protocatechuic aldehyde · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.84 | 0.93 | 63 | SAH, H6N |
| 2 | 325 | 0.83 | 0.93 | 63 | SAH, H6N |
| 3 | 188 | 0.56 | 0.79 | 32 | EDO |
| 4 | 176 | 0.52 | 0.78 | 31 | empty |
| 5 | 201 | 0.49 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 4346 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6I73 · Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine… · 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 Q9M602
- Elsewhere: RCSB PDB 6I73 · PDBe 6I73 · UniProt Q9M602
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.