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Crystal structure of human DUX4 homeodomains bound to A11G DNA mutant

Analyse Crystal structure of human DUX4 homeodomains bound to A11G DNA mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5ZFW
Type
protein + DNA
Length
160 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
3 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADouble homeobox protein 4-like protein 4protein12266% helix, 0% strandP0CJ87
DDNA (5'- D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*GP*AP*TP*CP*AP*CP*AP*CP*C)-3')dna19——
EDNA (5'- D(*GP*GP*TP*GP*TP*GP*AP*TP*CP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')dna19——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1780.720.9720empty
21290.450.7818empty
3560.360.7913empty

Interfaces

3 interfaces between chains.

  • A–E · 1157 Ų buried · 31 hydrogen bonds · protein-nucleic
  • A–D · 933 Ų buried · 26 hydrogen bonds · protein-nucleic
  • D–E · 846 Ų buried · 79 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5ZFW · Crystal structure of human DUX4 homeodomains bound to A11G 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

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