Research workbench
Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866A
Analyse Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LMT
- Type
- protein
- Length
- 1,012 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD2
- EC
- 2.1.1.357
- UniProt
- O96028
- Ligands
- Y6V, UNX
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 128 | 38% helix, 22% strand | O96028 |
| B | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 131 | 39% helix, 21% strand | O96028 |
| C | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 126 | 40% helix, 22% strand | O96028 |
| D | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 130 | 39% helix, 22% strand | O96028 |
| E | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 123 | 35% helix, 24% strand | O96028 |
| F | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 127 | 40% helix, 22% strand | O96028 |
| G | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 121 | 36% helix, 23% strand | O96028 |
| H | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 126 | 38% helix, 22% strand | O96028 |
Ligands and binding sites
- Y6V · ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide · ligand · 8 copies · chains A, H, B, C, D, E, F, G
- UNX · Unknown atom or ion · ion · 2 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.81 | 0.84 | 82 | empty |
| 2 | 342 | 0.73 | 0.85 | 30 | empty |
| 3 | 388 | 0.73 | 0.84 | 39 | empty |
| 4 | 142 | 0.65 | 0.87 | 22 | Y6V |
| 5 | 213 | 0.64 | 0.83 | 31 | Y6V |
Interfaces
12 interfaces between chains.
- A–H · 595 Ų buried · 1 hydrogen bond · protein-protein
- A–F · 589 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 561 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 561 Ų buried · 1 hydrogen bond · protein-protein
- G–H · 555 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7LMT · Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a · the same entry in another collection · chain H against H, 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 F against A, TM-score 0.97
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 7LMT · PDBe 7LMT · UniProt O96028
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