Research workbench
Crystal structure of human histone-lysine N-methyltransferase SMYD3 in complex with S-adenosyl-L-methionine
Analyse Crystal structure of human histone-lysine N-methyltransferase SMYD3 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MEK
- Type
- protein
- Length
- 423 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
- SAM, ZN
- Pockets
- 3 · best druggability 0.80
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 3 (EC 2.1.1.43) | protein | 423 | 50% helix, 13% 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.80 | 0.81 | 99 | SAM |
| 2 | 142 | 0.49 | 0.78 | 22 | empty |
| 3 | 139 | 0.48 | 0.79 | 27 | empty |
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3MEK · Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with… · 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 3MEK · PDBe 3MEK · UniProt Q9H7B4
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