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MolNFT v1 · #269 · protein + DNA

Qgsr (ZIF268 variant) zinc finger-DNA complex (gcac site)

1A1H · DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3'): “Qgsr (ZIF268 variant) zinc finger-DNA complex (gcac site)”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.61). MolNFT v1 #269 on GenesisL1: 3D structure, binding…

PDB
1A1H
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
3 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 42% 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——
AQgsr zinc finger peptideprotein8542% 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

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1870.610.9018empty
2770.490.8417empty
3700.480.8420empty

Interfaces

3 interfaces between chains.

  • B–A · 895 Ų buried · 21 hydrogen bonds · protein-nucleic
  • B–C · 474 Ų buried · 41 hydrogen bonds · nucleic-nucleic
  • C–A · 471 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 1A1H · Qgsr (ZIF268 variant) 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 0.95

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