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MolNFT v1 · #11350 · protein + DNA

ZIF268 D20A mutant bound to the gct DNA site

1JK2 · 5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3': “ZIF268 D20A mutant bound to the gct DNA site”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.61). MolNFT v1 #11350 on GenesisL1: 3D structure, binding sites and pockets…

PDB
1JK2
Type
protein + DNA
Length
107 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3'; 5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3'…
UniProt
P08046
Ligands
ZN
Pockets
2 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3'dna11——
C5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3'dna11——
AZIF268protein8540% helix, 14% strandP08046

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

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1780.610.9018empty
2670.610.9115empty

Interfaces

3 interfaces between chains.

  • B–A · 963 Ų buried · 21 hydrogen bonds · protein-nucleic
  • C–A · 510 Ų buried · 7 hydrogen bonds · protein-nucleic
  • B–C · 487 Ų buried · 39 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1JK2 · Zif268 D20A mutant bound to the GCT DNA site · the same entry in another collection · chain B against B, TM-score 1.00
  • P08046 · AlphaFold monomer V2.0 prediction for early growth response protein 1 (P08046) · a predicted model of the same protein · chain A against A, TM-score 0.94

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