MolNFT v1 · #74461 · protein
Human lysine methyltransferase SMYD3 in complex with adohcy (form III)
3OXG · Set and mynd domain-containing protein 3: “Human lysine methyltransferase SMYD3 in complex with adohcy (form III)”. X-ray diffraction, 2 ligands (SAH, ZN), 3 pockets (best druggability 0.78). MolNFT v1 #74461 on GenesisL1: 3D…
- PDB
- 3OXG
- Type
- protein
- Length
- 424 residues
- Chains
- 1
- 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
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Set and mynd domain-containing protein 3 (EC 2.1.1.43) | protein | 424 | 49% helix, 12% strand | Q9H7B4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.78 | 0.79 | 95 | empty |
| 2 | 258 | 0.62 | 0.81 | 38 | SAH |
| 3 | 74 | 0.37 | 0.77 | 14 | empty |
Compared structures
- 3OXG · human lysine methyltransferase Smyd3 in complex with AdoHcy (Form III) · 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 3OXG · PDBe 3OXG · UniProt Q9H7B4
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