Research workbench
Structure of Fragaria ananassa O-methyltransferase crystallized with PAS polypeptide
Analyse Structure of Fragaria ananassa O-methyltransferase crystallized with PAS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YJW
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Fragaria ananassa
- Molecule
- O-methyltransferase
- UniProt
- Q9M602
- Ligands
- SAH
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-methyltransferase | protein | 353 | 47% helix, 17% strand | Q9M602 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.84 | 0.93 | 63 | SAH, EDO |
| 2 | 365 | 0.84 | 0.93 | 63 | SAH |
| 3 | 199 | 0.55 | 0.78 | 22 | empty |
| 4 | 171 | 0.52 | 0.78 | 33 | EDO |
| 5 | 223 | 0.51 | 0.76 | 37 | EDO |
Interfaces
1 interface between chains.
- A–B · 4328 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YJW · Structure of fragaria ananassa O-methyltransferase crystallized with pas polypeptide · 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 6YJW · PDBe 6YJW · UniProt Q9M602
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