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MolNFT v1 · #63043 · protein + DNA

Crystal structure of a P53 core tetramer bound to DNA

3EXL · Mouse P53 core domain: “Crystal structure of a P53 core tetramer bound to DNA”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.26). MolNFT v1 #63043 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3EXL
Type
protein + DNA
Length
204 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Mouse P53 core domain; 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'…
UniProt
P02340
Ligands
ZN
Pockets
1 · best druggability 0.26

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 35% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMouse P53 core domainprotein19410% helix, 35% strandP02340
C5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'dna5——
D5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'dna5——

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A
  • FLC · Citrate anion · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1550.260.7414empty

Interfaces

3 interfaces between chains.

  • A–C · 325 Ų buried · 6 hydrogen bonds · protein-nucleic
  • C–D · 234 Ų buried · 20 hydrogen bonds · nucleic-nucleic
  • A–D · 73 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 3EXL · Crystal Structure of a p53 Core Tetramer Bound to DNA · the same entry in another collection · chain D against D, TM-score 1.00
  • P02340 · AlphaFold monomer V2.0 prediction for cellular tumor antigen P53 (P02340) · a predicted model of the same protein · chain A against A, TM-score 0.97

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