MolNFT v1 · #147287 · protein + DNA
Crystal structure of the double homeodomain of DUX4 in complex with DNA
6E8C · Double homeobox protein 4: “Crystal structure of the double homeodomain of DUX4 in complex with DNA”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #147287 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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