Research workbench
Crystal structure of human DUX4 homeodomains bound to A12C DNA mutant
Analyse Crystal structure of human DUX4 homeodomains bound to A12C DNA mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZFY
- Type
- protein + DNA
- Length
- 161 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double homeobox protein 4-like protein 4; DNA (5'…
- UniProt
- P0CJ87
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double homeobox protein 4-like protein 4 | protein | 123 | 68% helix, 0% strand | P0CJ87 |
| D | DNA (5'- D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*CP*TP*CP*AP*CP*AP*CP*C)-3') | dna | 19 | — | — |
| E | DNA (5'- D(*GP*GP*TP*GP*TP*GP*AP*GP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3') | dna | 19 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.75 | 0.96 | 23 | empty |
| 2 | 118 | 0.45 | 0.79 | 17 | empty |
| 3 | 50 | 0.35 | 0.80 | 13 | empty |
| 4 | 51 | 0.30 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1126 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 969 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–E · 850 Ų buried · 76 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ZFY · Crystal structure of human DUX4 homeodomains bound to A12C DNA mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P0CJ87 · AlphaFold monomer V2.0 prediction for double homeobox protein 4-like protein 4 (P0CJ87) · 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 P0CJ87
- Elsewhere: RCSB PDB 5ZFY · PDBe 5ZFY · UniProt P0CJ87
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