Research workbench
Papaver somniferum O-methyltransferase 1
Analyse Papaver somniferum O-methyltransferase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I6M
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase 1
- UniProt
- I3PLQ5
- Ligands
- SLX, SAH
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-methyltransferase 1 | protein | 343 | 49% helix, 15% strand | I3PLQ5 |
| B | O-methyltransferase 1 | protein | 357 | 48% helix, 15% strand | I3PLQ5 |
Ligands and binding sites
- SLX · (13aS)-3,10-dimethoxy-5,8,13,13a-tetrahydro-6H-isoquino[3,2-a]isoquinoline-2,9-diol · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.86 | 0.94 | 51 | SLX, SAH |
| 2 | 423 | 0.84 | 0.92 | 56 | SLX, SAH |
| 3 | 353 | 0.63 | 0.78 | 41 | empty |
| 4 | 236 | 0.53 | 0.77 | 28 | empty |
| 5 | 242 | 0.51 | 0.75 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 4111 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6I6M · Papaver somniferum O-methyltransferase 1 · 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 I3PLQ5
- Elsewhere: RCSB PDB 6I6M · PDBe 6I6M · UniProt I3PLQ5
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