Research workbench
Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives
Analyse Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LSU
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD2
- EC
- 2.1.1.43
- UniProt
- O96028
- Ligands
- SAM, ZN
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 231 | 17% helix, 26% strand | O96028 |
| B | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 222 | 16% helix, 29% strand | O96028 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.68 | 0.78 | 55 | SAM |
| 2 | 276 | 0.61 | 0.79 | 36 | SAM |
| 3 | 237 | 0.49 | 0.75 | 25 | empty |
| 4 | 68 | 0.39 | 0.79 | 16 | empty |
| 5 | 96 | 0.36 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 456 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5LSU · Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin… · the same entry in another collection · chain A against A, TM-score 1.00
- O96028 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase NSD2 (O96028) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 O96028
- Elsewhere: RCSB PDB 5LSU · PDBe 5LSU · UniProt O96028
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