MolNFT v1 · #144037 · protein
Crystal structure of SETDB1 with a modified H3 peptide
6BHD · Histone-lysine N-methyltransferase SETDB1: “Crystal structure of SETDB1 with a modified H3 peptide”. X-ray diffraction, 2 ligands (NA, UNX), 3 pockets (best druggability 0.41). MolNFT v1 #144037 on GenesisL1: 3D structure, binding…
- PDB
- 6BHD
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETDB1; Histone H3.1
- EC
- 2.1.1.43
- UniProt
- Q15047, P68431
- Ligands
- NA, UNX
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETDB1 (EC 2.1.1.43) | protein | 217 | 14% helix, 45% strand | Q15047 |
| B | Histone H3.1 | protein | 12 | 0% helix, 8% strand | P68431 |
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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.41 | 0.79 | 18 | UNX |
| 2 | 75 | 0.36 | 0.76 | 17 | UNX |
| 3 | 72 | 0.36 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation, methylation).
Compared structures
- 6BHD · Crystal structure of SETDB1 with a modified H3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q15047 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETDB1 (Q15047) · 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 Q15047
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 6BHD · PDBe 6BHD · UniProt Q15047 · UniProt P68431
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