MolNFT v1 · #152086 · protein
Structure of fragaria ananassa O-methyltransferase in complex with S- adenosylhomocysteine
6I71: “Structure of fragaria ananassa O-methyltransferase in complex with S- adenosylhomocysteine”. X-ray diffraction, 2 ligands (SAH, SO4), 12 pockets (best druggability 0.85). MolNFT v1 #152086 on GenesisL1: 3D structure, binding sites…
- PDB
- 6I71
- 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, SO4
- Pockets
- 12 · best druggability 0.85
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
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.85 | 0.95 | 60 | SAH, EDO |
| 2 | 322 | 0.84 | 0.94 | 62 | SAH, EDO |
| 3 | 51 | 0.58 | 0.92 | 18 | empty |
| 4 | 194 | 0.57 | 0.80 | 24 | EDO |
| 5 | 244 | 0.54 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 4405 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6I71 · 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 6I71 · PDBe 6I71 · UniProt Q9M602
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