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Crystal structure of human histone-lysine N-methyltransferase NSD1 set domain in complex with S-adenosyl-L-methionine
Analyse Crystal structure of human histone-lysine N-methyltransferase NSD1 set domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OOI
- Type
- protein
- Length
- 232 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
- EC
- 2.1.1.43
- UniProt
- Q96L73
- Ligands
- SAM, ZN, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific (EC 2.1.1.43) | protein | 232 | 19% helix, 27% strand | Q96L73 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
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 | 353 | 0.68 | 0.81 | 52 | SAM |
| 2 | 53 | 0.32 | 0.78 | 19 | empty |
| 3 | 61 | 0.30 | 0.75 | 15 | empty |
Compared structures
- 3OOI · Crystal Structure of Human Histone-Lysine N-methyltransferase NSD1 SET domain in Complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96L73 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-36… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q96L73
- Elsewhere: RCSB PDB 3OOI · PDBe 3OOI · UniProt Q96L73
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