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Wilms tumor protein (WT1) Q369R ZNF2-4 in complex with DNA

Analyse Wilms tumor protein (WT1) Q369R ZNF2-4 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5KL6
Type
protein + DNA
Length
109 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Wilms tumor protein; DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*GP*GP*T)-3'); DNA…
UniProt
P19544
Ligands
ZN
Pockets
3 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AWilms tumor proteinprotein8741% helix, 14% strandP19544
BDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*GP*GP*T)-3')dna11——
CDNA (5'-D(*TP*AP*CP*CP*CP*CP*CP*AP*CP*GP*C)-3')dna11——

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
1810.660.9219empty
21030.590.8714empty
3540.280.7513empty

Interfaces

3 interfaces between chains.

  • A–B · 941 Ų buried · 25 hydrogen bonds · protein-nucleic
  • B–C · 484 Ų buried · 41 hydrogen bonds · nucleic-nucleic
  • A–C · 484 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 5KL6 · Wilms Tumor Protein (WT1) Q369R ZnF2-4 in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P19544 · AlphaFold monomer V2.0 prediction for wilms tumor protein (P19544) · a predicted model of the same protein · chain A against A, TM-score 0.92

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