MolNFT v1 · #79872 · protein
Structure of SMYD2 in complex with SAM
3TG4 · N-lysine methyltransferase SMYD2: “Structure of SMYD2 in complex with SAM”. X-ray diffraction, 2 ligands (SAM, ZN), 4 pockets (best druggability 0.80). MolNFT v1 #79872 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3TG4
- Type
- protein
- Length
- 427 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4
- Ligands
- SAM, ZN
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% 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 | 427 | 51% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.80 | 0.81 | 106 | SAM, GOL |
| 2 | 73 | 0.40 | 0.79 | 17 | empty |
| 3 | 68 | 0.35 | 0.77 | 12 | GOL |
| 4 | 85 | 0.34 | 0.74 | 14 | empty |
Compared structures
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 3TG4 · PDBe 3TG4 · UniProt Q9NRG4
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