MolNFT v1 · #71143 · protein
SET7/9 Y245A in complex with TAF10-K189ME3 peptide and adohcy
3M5A · Histone-lysine N-methyltransferase SETD7: “SET7/9 Y245A in complex with TAF10-K189ME3 peptide and adohcy”. X-ray diffraction, 3 ligands (ACE, SAH, CO), 1 pocket (best druggability 0.42). MolNFT v1 #71143 on GenesisL1: 3D structure…
- PDB
- 3M5A
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD7; TAF10-K189ME3 peptide
- EC
- 2.1.1.43
- UniProt
- Q8WTS6
- Ligands
- ACE, SAH, CO
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 246 | 11% helix, 37% strand | Q8WTS6 |
| B | TAF10-K189ME3 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
- CO · Cobalt (II) ion · metal · 7 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.42 | 0.76 | 23 | SAH |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, methylation).
Compared structures
- 3M5A · SET7/9 Y245A in complex with TAF10-K189me3 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 0.99
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 Q8WTS6
- Elsewhere: RCSB PDB 3M5A · PDBe 3M5A · UniProt Q8WTS6
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