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Determination of the NMR solution structure of an antennapedia homeodomain-DNA complex

Analyse Determination of the NMR solution structure of an antennapedia homeodomain-DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1AHD
Type
protein + DNA
Length
96 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'); DNA…
UniProt
Q24645
Pockets
3 · best druggability 0.43

Structure

solution nmr · 3 distinct chains · 59% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')dna14——
BDNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')dna14——
PHomeotic protein antennapediaprotein6859% helix, 0% strandQ24645

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11150.430.7814empty
21080.410.7717empty
3500.260.7411empty

Interfaces

3 interfaces between chains.

  • A–P · 815 Ų buried · 32 hydrogen bonds · protein-nucleic
  • A–B · 639 Ų buried · 65 hydrogen bonds · nucleic-nucleic
  • B–P · 494 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 1AHD · Determination of the NMR solution structure of an antennapedia homeodomain-DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
  • Q24645 · AlphaFold monomer V2.0 prediction for homeotic protein antennapedia (Q24645) · a predicted model of the same protein · chain P against A, TM-score 0.76

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