Research workbench
Crystal structure of the set domain of human histone-lysine N- methyltransferase SUV420H1 in complex with S-adenosyl-L-methionine
Analyse Crystal structure of the set domain of human histone-lysine N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S8P
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SUV420H1
- EC
- 2.1.1.43
- UniProt
- Q4FZB7
- Ligands
- SAM, ZN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SUV420H1 (EC 2.1.1.43) | protein | 233 | 39% helix, 23% strand | Q4FZB7 |
| B | Histone-lysine N-methyltransferase SUV420H1 (EC 2.1.1.43) | protein | 238 | 37% helix, 23% strand | Q4FZB7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.78 | 0.80 | 92 | SAM |
| 2 | 200 | 0.61 | 0.82 | 31 | SAM |
| 3 | 111 | 0.51 | 0.81 | 18 | empty |
| 4 | 70 | 0.34 | 0.76 | 14 | empty |
| 5 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 777 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3S8P · Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1… · the same entry in another collection · chain B against B, TM-score 1.00
- Q4FZB7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase KMT5B (Q4FZB7) · 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 Q4FZB7
- Elsewhere: RCSB PDB 3S8P · PDBe 3S8P · UniProt Q4FZB7
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