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Mouse KLF4 ZNF1-3 and TPG/CPA sequence DNA complex structure

Analyse Mouse KLF4 ZNF1-3 and TPG/CPA sequence DNA complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5KE6
Type
protein + DNA
Length
105 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Krueppel-like factor 4; DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3'); DNA…
UniProt
Q60793
Ligands
ZN
Pockets
3 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AKrueppel-like factor 4protein8539% helix, 14% strandQ60793
BDNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3')dna10——
CDNA (5'-D(*GP*CP*CP*AP*CP*AP*CP*CP*TP*C)-3')dna10——

Ligands and binding sites

  • ZN · Zinc ion · metal · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11220.630.8823empty
21480.630.8629empty
3560.280.7514empty

Interfaces

3 interfaces between chains.

  • A–B · 645 Ų buried · 13 hydrogen bonds · protein-nucleic
  • B–C · 442 Ų buried · 34 hydrogen bonds · nucleic-nucleic
  • A–C · 435 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 5KE6 · mouse Klf4 ZnF1-3 and TpG/CpA sequence DNA complex structure · the same entry in another collection · chain A against A, TM-score 1.00
  • Q60793 · AlphaFold monomer V2.0 prediction for krueppel-like factor 4 (Q60793) · a predicted model of the same protein · chain A against A, TM-score 0.91

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