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Diversity in DNA recognition by P53 revealed by crystal structures with hoogsteen base pairs (P53-DNA complex 1)

Analyse Diversity in DNA recognition by P53 revealed by crystal structures with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3IGL
Type
protein + DNA
Length
208 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cellular tumor antigen P53; DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
UniProt
P04637
Ligands
ZN
Pockets
2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACellular tumor antigen P53protein19712% helix, 34% strandP04637
BDNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')dna11——

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A
  • EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1930.370.7521empty
2570.240.7215empty

Interfaces

1 interface between chains.

  • A–B · 233 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 3IGL · Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base… · the same entry in another collection · chain A against A, TM-score 1.00

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