Research workbench
Crystal structure of DUX4 HD1-HD2 domain complexed with erg sites
Analyse Crystal structure of DUX4 HD1-HD2 domain complexed with erg sites in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DW5
- Type
- protein + DNA
- Length
- 346 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double homeobox protein 4-like protein 2; DNA (5'…
- UniProt
- P0CJ85
- Ligands
- BR
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Double homeobox protein 4-like protein 2 | protein | 131 | 64% helix, 0% strand | P0CJ85 |
| E, C | DNA (5'- D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)- 3') | dna | 21 | — | — |
| F, D | DNA (5'- D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)- 3') | dna | 21 | — | — |
Ligands and binding sites
- BR · Bromide ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.78 | 0.96 | 24 | empty |
| 2 | 225 | 0.75 | 0.90 | 30 | empty |
| 3 | 233 | 0.53 | 0.77 | 30 | empty |
| 4 | 150 | 0.48 | 0.78 | 24 | empty |
| 5 | 125 | 0.40 | 0.75 | 21 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1423 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- E–F · 919 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–C · 599 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–E · 584 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 7DW5 · Crystal structure of DUX4 HD1-HD2 domain complexed with ERG sites · the same entry in another collection · chain F against F, TM-score 1.00
- P0CJ85 · AlphaFold monomer V2.0 prediction for double homeobox protein 4-like protein 2 (P0CJ85) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 P0CJ85
- Elsewhere: RCSB PDB 7DW5 · PDBe 7DW5 · UniProt P0CJ85
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