MolNFT v1 · #154916 · protein
NSD1 set domain in complex with BT3 and SAM
6KQQ · Histone-lysine N-methyltransferase, H3 lysine-36 and H4…: “NSD1 set domain in complex with BT3 and SAM”. X-ray diffraction, 5 ligands (SAM, DQL, DW9), 8 pockets (best druggability 0.73). MolNFT v1 #154916 on GenesisL1: 3D structure…
- PDB
- 6KQQ
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- 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, DQL, DW9, ZN, CA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 28% 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 | 223 | 17% helix, 27% strand | Q96L73 |
| B | Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific (EC 2.1.1.43) | protein | 219 | 16% helix, 29% strand | Q96L73 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- DQL · 2-azanyl-6-sulfanyl-1,3-benzothiazol-4-ol · ligand · 2 copies · chains A, B
- DW9 · 2-azanyl-6-[(2-azanyl-4-oxidanyl-1,3-benzothiazol-6-yl)disulfanyl]-1,3-benzothiazol-4-ol · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.73 | 0.81 | 76 | SAM, DQL, DW9, GOL |
| 2 | 479 | 0.65 | 0.78 | 50 | CA |
| 3 | 264 | 0.64 | 0.82 | 38 | SAM, DQL |
| 4 | 95 | 0.42 | 0.78 | 23 | empty |
| 5 | 87 | 0.41 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 772 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 6KQQ · PDBe 6KQQ · UniProt Q96L73
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