MolNFT v1 · #165839 · protein + DNA
Crystal structure of the double homeodomain of DUX4 in complex with a DNA aptamer containing bulge and loop
6U82 · Double homeobox protein 4: “Crystal structure of the double homeodomain of DUX4 in complex with a DNA aptamer containing bulge and loop”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #165839 on GenesisL1: 3D…
- PDB
- 6U82
- Type
- protein + DNA
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double homeobox protein 4; DNA (38-mer)
- UniProt
- Q9UBX2
- Pockets
- 5 · best druggability 0.72
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 | 132 | 61% helix, 0% strand | Q9UBX2 |
| B, E | DNA (38-mer) | dna | 38 | — | — |
| D | Double homeobox protein 4 | protein | 134 | 60% helix, 0% strand | Q9UBX2 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.72 | 0.92 | 26 | empty |
| 2 | 124 | 0.68 | 0.90 | 26 | empty |
| 3 | 71 | 0.40 | 0.80 | 20 | empty |
| 4 | 75 | 0.39 | 0.79 | 15 | empty |
| 5 | 50 | 0.22 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2113 Ų buried · 51 hydrogen bonds · protein-nucleic
- D–E · 2101 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–E · 200 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 6U82 · 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 0.98
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 6U82 · PDBe 6U82 · UniProt Q9UBX2
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