Research workbench
Crystal structure of histone lysine methyltransferase SMYD2 in complex with the methyltransferase inhibitor sinefungin
Analyse Crystal structure of histone lysine methyltransferase SMYD2 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QWW
- Type
- protein
- Length
- 430 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Set and mynd domain-containing protein 2
- UniProt
- Q8R5A0
- Ligands
- SFG, ZN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Set and mynd domain-containing protein 2 | protein | 430 | 50% helix, 13% strand | Q8R5A0 |
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 | 999 | 0.77 | 0.78 | 96 | empty |
| 2 | 152 | 0.60 | 0.83 | 25 | SFG |
| 3 | 63 | 0.35 | 0.78 | 15 | empty |
Compared structures
- 3QWW · Crystal structure of histone lysine methyltransferase SmyD2 in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8R5A0 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q8R5A0) · 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 Q8R5A0
- Elsewhere: RCSB PDB 3QWW · PDBe 3QWW · UniProt Q8R5A0
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