Research workbench
Crystal structure of the double homeodomain of DUX4 in complex with DNA
Analyse Crystal structure of the double homeodomain of DUX4 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E8C
- Type
- protein + DNA
- Length
- 169 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double homeobox protein 4; DNA (5'- D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)…
- UniProt
- Q9UBX2
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double homeobox protein 4 | protein | 135 | 61% helix, 0% strand | Q9UBX2 |
| B | DNA (5'- D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3') | dna | 17 | — | — |
| C | DNA (5'- D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3') | dna | 17 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.69 | 0.96 | 20 | empty |
| 2 | 67 | 0.39 | 0.80 | 19 | empty |
| 3 | 110 | 0.38 | 0.75 | 17 | empty |
| 4 | 106 | 0.36 | 0.75 | 16 | empty |
| 5 | 61 | 0.34 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1214 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 1016 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 750 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6E8C · Crystal structure of the double homeodomain of DUX4 in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBX2 · AlphaFold monomer V2.0 prediction for double homeobox protein 4 (Q9UBX2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 6E8C · PDBe 6E8C · UniProt Q9UBX2
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