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MolNFT v1 · #3884 · protein + DNA

DNA recognition by GAL4: structure of a PROTEIN/DNA complex

1D66 · DNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*…: “DNA recognition by GAL4: structure of a PROTEIN/DNA complex”. X-ray diffraction, 1 ligand (CD), 1 pocket (best druggability 0.58). MolNFT v1 #3884 on GenesisL1: 3D…

PDB
1D66
Type
protein + DNA
Length
152 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3'); DNA (5'…
UniProt
P04386
Ligands
CD
Pockets
1 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
DDNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3')dna19——
EDNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*TP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3')dna19——
A, BProtein (GAL4)protein5740% helix, 0% strandP04386

Ligands and binding sites

  • CD · Cadmium ion · metal · 4 copies · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13270.580.7839empty

Interfaces

6 interfaces between chains.

  • D–E · 867 Ų buried · 100 hydrogen bonds · nucleic-nucleic
  • A–B · 660 Ų buried · 7 hydrogen bonds · protein-protein
  • E–A · 485 Ų buried · 6 hydrogen bonds · protein-nucleic
  • D–B · 449 Ų buried · 8 hydrogen bonds · protein-nucleic
  • D–A · 275 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 1D66 · DNA recognition by GAL4: structure of a PROTEIN/DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
  • P04386 · AlphaFold monomer V2.0 prediction for regulatory protein GAL4 (P04386) · a predicted model of the same protein · chain A against A, TM-score 0.70

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