Research workbench
norbelladine 4'-O-methyltransferase complexed with Mg and SAH
Analyse norbelladine 4'-O-methyltransferase complexed with Mg and SAH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8XE3
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.72
- Source
- Narcissus pseudonarcissus MK-2014
- Molecule
- Norbelladine 4'-O-methyltransferase
- UniProt
- A0A077EWA5
- Ligands
- SAH, MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.72 · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Norbelladine 4'-O-methyltransferase | protein | 239 | 51% helix, 19% strand | A0A077EWA5 |
| B | Norbelladine 4'-O-methyltransferase | protein | 240 | 48% helix, 19% strand | A0A077EWA5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.74 | 0.80 | 65 | SAH |
| 2 | 627 | 0.74 | 0.80 | 61 | SAH |
| 3 | 99 | 0.50 | 0.81 | 19 | empty |
| 4 | 87 | 0.48 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2084 Ų buried · 27 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 A0A077EWA5
- Elsewhere: RCSB PDB 8XE3 · PDBe 8XE3 · UniProt A0A077EWA5
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