Research workbench
PWWP1 domain of NSD2 in complex with MR837
Analyse PWWP1 domain of NSD2 in complex with MR837 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UE6
- Type
- protein
- Length
- 965 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD2
- EC
- 2.1.1.43
- UniProt
- O96028
- Ligands
- Q5D, UNX
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 132 | 41% helix, 21% strand | O96028 |
| B | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 123 | 34% helix, 23% strand | O96028 |
| C | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 107 | 30% helix, 26% strand | O96028 |
| D | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 120 | 38% helix, 22% strand | O96028 |
| E | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 126 | 40% helix, 24% strand | O96028 |
| F | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 108 | 35% helix, 26% strand | O96028 |
| G | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 121 | 36% helix, 25% strand | O96028 |
| H | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 128 | 39% helix, 22% strand | O96028 |
Ligands and binding sites
- Q5D · 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl) methyl]benzamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- UNX · Unknown atom or ion · ion · 51 copies · chains A, B, C, D, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.67 | 0.88 | 24 | Q5D, UNX |
| 2 | 150 | 0.66 | 0.87 | 24 | Q5D, UNX |
| 3 | 214 | 0.66 | 0.84 | 30 | Q5D |
| 4 | 147 | 0.66 | 0.87 | 24 | Q5D |
| 5 | 136 | 0.65 | 0.87 | 22 | Q5D, UNX |
Interfaces
9 interfaces between chains.
- G–H · 555 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 506 Ų buried · 0 hydrogen bonds · protein-protein
- E–H · 506 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 506 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 492 Ų buried · 1 hydrogen bond · protein-protein
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 O96028
- Elsewhere: RCSB PDB 6UE6 · PDBe 6UE6 · UniProt O96028
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