MolNFT v1 · #78381 · protein
Structural basis of substrate methylation and inhibition of SMYD2
3S7D · N-lysine methyltransferase SMYD2: “Structural basis of substrate methylation and inhibition of SMYD2”. X-ray diffraction, 2 ligands (SAH, ZN), 9 pockets (best druggability 0.62). MolNFT v1 #78381 on GenesisL1: 3D structure, binding…
- PDB
- 3S7D
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2; Monomethylated P53 peptide
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4
- Ligands
- SAH, ZN
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 429 | 51% helix, 14% strand | Q9NRG4 |
| I | Monomethylated P53 peptide | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, I
- ZN · Zinc ion · metal · 3 copies · chains A
- BU3 · (R,R)-2,3-butanediol · additive · 3 copies · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.62 | 0.77 | 40 | BU3 |
| 2 | 169 | 0.59 | 0.82 | 31 | SAH |
| 3 | 56 | 0.54 | 0.88 | 23 | empty |
| 4 | 133 | 0.43 | 0.76 | 16 | empty |
| 5 | 118 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–I · 684 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3S7D · Structural Basis of Substrate Methylation and Inhibition of SMYD2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRG4 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q9NRG4) · a predicted model of the same protein · 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 Q9NRG4
- Elsewhere: RCSB PDB 3S7D · PDBe 3S7D · UniProt Q9NRG4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.