Research workbench
Crystal structure of DUX4 HD2 domain associated with erg DNA binding site
Analyse Crystal structure of DUX4 HD2 domain associated with erg DNA binding site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A8R
- Type
- protein + DNA
- Length
- 136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double homeobox protein 4; DNA (5'-D(P*TP*GP*AP*TP*GP*AP*GP*AP*TP*T)-3'); DNA…
- UniProt
- Q9UBX2
- Pockets
- 2 · best druggability 0.29
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Double homeobox protein 4 | protein | 58 | 66% helix, 0% strand | Q9UBX2 |
| E | DNA (5'-D(P*TP*GP*AP*TP*GP*AP*GP*AP*TP*T)-3') | dna | 10 | — | — |
| F | DNA (5'-D(P*AP*AP*TP*CP*TP*CP*AP*TP*CP*A)-3') | dna | 10 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.29 | 0.74 | 15 | empty |
| 2 | 68 | 0.26 | 0.72 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–E · 584 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–F · 439 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- A–F · 330 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–F · 134 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6A8R · Crystal structure of DUX4 HD2 domain associated with ERG DNA binding site · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UBX2 · AlphaFold monomer V2.0 prediction for double homeobox protein 4 (Q9UBX2) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q9UBX2
- Elsewhere: RCSB PDB 6A8R · PDBe 6A8R · UniProt Q9UBX2
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