Research workbench
Human lysine methyltransferase SMYD3 in complex with adohcy (form I)
Analyse Human lysine methyltransferase SMYD3 in complex with adohcy (form I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OXF
- Type
- protein
- Length
- 851 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Set and mynd domain-containing protein 3
- EC
- 2.1.1.43
- UniProt
- Q9H7B4
- Ligands
- SAH, ZN
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Set and mynd domain-containing protein 3 (EC 2.1.1.43) | protein | 426 | 50% helix, 13% strand | Q9H7B4 |
| B | Set and mynd domain-containing protein 3 (EC 2.1.1.43) | protein | 425 | 48% helix, 13% strand | Q9H7B4 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.84 | 0.85 | 99 | SAH |
| 2 | 1119 | 0.79 | 0.81 | 107 | SAH |
| 3 | 226 | 0.55 | 0.78 | 35 | empty |
| 4 | 207 | 0.53 | 0.77 | 35 | empty |
| 5 | 102 | 0.35 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 441 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3OXF · Human lysine methyltransferase Smyd3 in complex with AdoHcy (Form I) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H7B4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9H7B4
- Elsewhere: RCSB PDB 3OXF · PDBe 3OXF · UniProt Q9H7B4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.