Research workbench
Crystal structure of SMYD3 in complex with methyltransferase inhibitor sinefungin
Analyse Crystal structure of SMYD3 in complex with methyltransferase inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PDN
- Type
- protein
- Length
- 427 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
- SFG, ZN, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% 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 | 427 | 51% helix, 13% strand | Q9H7B4 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.80 | 0.81 | 98 | SFG, GOL |
| 2 | 147 | 0.52 | 0.80 | 26 | empty |
| 3 | 106 | 0.44 | 0.79 | 24 | empty |
| 4 | 53 | 0.32 | 0.76 | 13 | GOL |
| 5 | 64 | 0.28 | 0.73 | 13 | empty |
Compared structures
- 3PDN · Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin · 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 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 Q9H7B4
- Elsewhere: RCSB PDB 3PDN · PDBe 3PDN · UniProt Q9H7B4
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