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ZIF268 zinc finger-DNA complex (gcac site)

Analyse ZIF268 zinc finger-DNA complex (gcac site) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1A1L
Type
protein + DNA
Length
107 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3'); DNA…
UniProt
P08046
Ligands
ZN
Pockets
2 · best druggability 0.61

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3')dna11——
CDNA (5'-D(*TP*GP*TP*GP*CP*CP*CP*AP*CP*GP*C)-3')dna11——
AProtein (ZIF268 zinc finger peptide)protein8540% 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
1840.610.9019empty
21000.560.8516empty

Interfaces

3 interfaces between chains.

  • B–A · 952 Ų buried · 26 hydrogen bonds · protein-nucleic
  • B–C · 476 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • C–A · 437 Ų buried · 5 hydrogen bonds · protein-nucleic

Compared structures

  • 1A1L · ZIF268 zinc finger-DNA complex (gcac 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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