Research workbench
O-Methyltransferase Plu4890 in complex with SAH and AQ-284b
Analyse O-Methyltransferase Plu4890 in complex with SAH and AQ-284b in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BIH
- Type
- protein
- Length
- 3,828 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Photorhabdus laumondii subsp. laumondii TTO1
- Molecule
- Methyltransferase Plu4890
- UniProt
- A0A6L9JR93
- Ligands
- SAH, QOT, NA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Methyltransferase Plu4890 | protein | 319 | 49% helix, 18% strand | A0A6L9JR93 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- QOT · 3,8-dimethoxy-1-oxidanyl-anthracene-9,10-dione · ligand · 9 copies · chains A, L, B, E, C, G, D, K, F, H, I, J
- NA · Sodium ion · metal · 2 copies · chains H, D, K
- CL · Chloride ion · ion · 4 copies · chains A, C, G
- GOL · Glycerol · additive · 2 copies · chains C, G, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.85 | 0.86 | 110 | SAH, QOT |
| 2 | 481 | 0.85 | 0.91 | 69 | SAH, QOT |
| 3 | 495 | 0.84 | 0.90 | 69 | SAH, QOT |
| 4 | 672 | 0.84 | 0.88 | 95 | SAH, QOT, GOL |
| 5 | 541 | 0.83 | 0.89 | 82 | SAH, QOT |
Interfaces
33 interfaces between chains.
- F–H · 3148 Ų buried · 59 hydrogen bonds · protein-protein
- D–K · 3136 Ų buried · 56 hydrogen bonds · protein-protein
- C–G · 3119 Ų buried · 57 hydrogen bonds · protein-protein
- B–E · 3100 Ų buried · 56 hydrogen bonds · protein-protein
- A–L · 3097 Ų buried · 58 hydrogen bonds · protein-protein
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 A0A6L9JR93
- Elsewhere: RCSB PDB 8BIH · PDBe 8BIH · UniProt A0A6L9JR93
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