MolNFT v1 · #149546 · protein
X-ray structure of seleno-methionine labelled NSD3-PWWP1
6G3P · Histone-lysine N-methyltransferase NSD3: “X-ray structure of seleno-methionine labelled NSD3-PWWP1”. X-ray diffraction, 6 pockets (best druggability 0.60). MolNFT v1 #149546 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6G3P
- Type
- protein
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD3
- EC
- 2.1.1.43
- UniProt
- Q9BZ95
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 124 | 34% helix, 23% strand | Q9BZ95 |
| B | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 128 | 38% helix, 22% strand | Q9BZ95 |
| C | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 111 | 32% helix, 24% strand | Q9BZ95 |
| D | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 110 | 35% helix, 25% strand | Q9BZ95 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.60 | 0.78 | 28 | empty |
| 2 | 275 | 0.57 | 0.78 | 26 | empty |
| 3 | 344 | 0.56 | 0.75 | 44 | empty |
| 4 | 126 | 0.50 | 0.80 | 21 | empty |
| 5 | 169 | 0.47 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1293 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 779 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 296 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 266 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6G3P · X-ray structure of seleno-methionine labelled NSD3-PWWP1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BZ95 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase NSD3 (Q9BZ95) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q9BZ95
- Elsewhere: RCSB PDB 6G3P · PDBe 6G3P · UniProt Q9BZ95
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