MolNFT v1 · #165838 · protein + DNA
Crystal structure of the double homeodomain of DUX4 in complex with a DNA aptamer
6U81 · Double homeobox protein 4: “Crystal structure of the double homeodomain of DUX4 in complex with a DNA aptamer”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #165838 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6U81
- 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 0.70
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double homeobox protein 4 | protein | 132 | 63% 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*CP*CP*CP*AP*TP*TP*AP*CP*GP*C)-3') | dna | 20 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 70 | 0.70 | 0.96 | 18 | empty |
| 2 | 114 | 0.41 | 0.77 | 18 | EDO |
| 3 | 71 | 0.34 | 0.77 | 18 | empty |
| 4 | 71 | 0.33 | 0.76 | 14 | empty |
| 5 | 51 | 0.24 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 997 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 942 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 451 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 6U81 · Crystal Structure of the Double Homeodomain of DUX4 in Complex with a DNA aptamer · 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 0.99
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 6U81 · PDBe 6U81 · UniProt Q9UBX2
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