Research workbench
X-ray structure of NSD3-PWWP1
Analyse X-ray structure of NSD3-PWWP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G3T
- Type
- protein
- Length
- 457 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
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 116 | 33% helix, 23% strand | Q9BZ95 |
| B | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 115 | 33% helix, 23% strand | Q9BZ95 |
| C | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 112 | 34% helix, 24% strand | Q9BZ95 |
| D | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 114 | 33% helix, 24% strand | Q9BZ95 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.61 | 0.85 | 20 | EPE |
| 2 | 498 | 0.61 | 0.75 | 52 | empty |
| 3 | 394 | 0.60 | 0.76 | 33 | empty |
| 4 | 302 | 0.59 | 0.78 | 29 | empty |
| 5 | 138 | 0.58 | 0.83 | 20 | EPE |
Interfaces
4 interfaces between chains.
- C–D · 805 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 797 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 10 Ų buried · 0 hydrogen bonds · 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 Q9BZ95
- Elsewhere: RCSB PDB 6G3T · PDBe 6G3T · UniProt Q9BZ95
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