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Crystal structure of DNA-bound DUX4-HD2

Analyse Crystal structure of DNA-bound DUX4-HD2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5Z2T
Type
protein + DNA
Length
133 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Double homeobox protein 4; 5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*TP*T)-3'…
UniProt
Q9UBX2
Pockets
2 · best druggability 0.51

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
CDouble homeobox protein 4protein5372% helix, 0% strandQ9UBX2
E5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*TP*T)-3'dna13——
F5'-D(P*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'dna13——
DDouble homeobox protein 4protein5470% helix, 0% strandQ9UBX2

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11590.510.7926empty
22130.490.7523empty

Interfaces

5 interfaces between chains.

  • E–F · 561 Ų buried · 52 hydrogen bonds · nucleic-nucleic
  • E–D · 401 Ų buried · 10 hydrogen bonds · protein-nucleic
  • C–E · 336 Ų buried · 6 hydrogen bonds · protein-nucleic
  • F–D · 297 Ų buried · 5 hydrogen bonds · protein-nucleic
  • C–F · 247 Ų buried · 2 hydrogen bonds · protein-nucleic

Compared structures

  • 5Z2T · Crystal structure of DNA-bound DUX4-HD2 · the same entry in another collection · chain C against C, TM-score 1.00
  • Q9UBX2 · AlphaFold monomer V2.0 prediction for double homeobox protein 4 (Q9UBX2) · a predicted model of the same protein · chain C against A, TM-score 0.94

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