Research workbench
Crystal structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9ME3 peptide
Analyse Crystal structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9ME3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GNG
- Type
- protein
- Length
- 212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD3; Histone H3.3
- EC
- 2.1.1.43
- UniProt
- Q9BZ95, P84243
- Ligands
- ZN
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 95 | 6% helix, 18% strand | Q9BZ95 |
| B, F | Histone H3.3 | protein | 10 | 0% helix, 30% strand | P84243 |
| D | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 97 | 9% helix, 20% strand | Q9BZ95 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 685 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 670 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 266 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4GNG · Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.93
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain B against A, TM-score 0.44
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
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 4GNG · PDBe 4GNG · UniProt Q9BZ95 · UniProt P84243
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