Research workbench
SET7/9 Y245A in complex with TAF10-K189ME1 peptide and adohcy
Analyse SET7/9 Y245A in complex with TAF10-K189ME1 peptide and adohcy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M58
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD7; TAF10-K189ME1 peptide
- EC
- 2.1.1.43
- UniProt
- Q8WTS6
- Ligands
- ACE, SAH, SO4
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 253 | 12% helix, 36% strand | Q8WTS6 |
| B | TAF10-K189ME1 peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.47 | 0.76 | 28 | SAH |
| 2 | 57 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 697 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, methylation).
Compared structures
- 3M58 · SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WTS6 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD7 (Q8WTS6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8WTS6
- Elsewhere: RCSB PDB 3M58 · PDBe 3M58 · UniProt Q8WTS6
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