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Structural basis of prospero-DNA interaction; implications for transcription regulation in developing cells

Analyse Structural basis of prospero-DNA interaction; implications for transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1XPX
Type
protein + DNA
Length
164 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'; 5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'; Protein…
UniProt
P29617
Pockets
3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
D5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'dna10——
C5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'dna10——
AProtein prosperoprotein14465% helix, 0% strandP29617

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12760.540.7626empty
21270.520.8115empty
3700.470.8319empty

Interfaces

3 interfaces between chains.

  • D–C · 458 Ų buried · 52 hydrogen bonds · nucleic-nucleic
  • D–A · 282 Ų buried · 4 hydrogen bonds · protein-nucleic
  • C–A · 218 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 1XPX · Structural basis of prospero-DNA interaction; implications for transcription regulation… · the same entry in another collection · chain D against D, TM-score 1.00
  • P29617 · AlphaFold monomer V2.0 prediction for homeobox protein prospero (P29617) · a predicted model of the same protein · chain A against A, TM-score 0.97

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