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MolNFT v1 · #156120 · protein + DNA

DNA bound antitoxin HIGA3

6LTY · Putative antitoxin HIGA3: “DNA bound antitoxin HIGA3”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #156120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6LTY
Type
protein + DNA
Length
196 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Putative antitoxin HIGA3; DNA (5'- D(P*CP*CP*AP*CP*GP*AP*GP*AP*TP*AP*TP*AP*AP*CP*CP*TP*AP*…
UniProt
O53333
Pockets
4 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BPutative antitoxin HIGA3protein7844% helix, 18% strandO53333
CDNA (5'- D(P*CP*CP*AP*CP*GP*AP*GP*AP*TP*AP*TP*AP*AP*CP*CP*TP*AP*GP*AP*G)-3')dna20——
DDNA (5'- D(P*CP*TP*CP*TP*AP*GP*GP*TP*TP*AP*TP*AP*TP*CP*TP*CP*GP*TP*GP*G)-3')dna20——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13950.620.7843empty
2820.530.8518empty
3800.350.7617empty
4640.300.7516empty

Interfaces

6 interfaces between chains.

  • A–B · 1667 Ų buried · 22 hydrogen bonds · protein-protein
  • C–D · 855 Ų buried · 58 hydrogen bonds · nucleic-nucleic
  • B–D · 405 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–C · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
  • A–D · 355 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 6LTY · DNA bound antitoxin HigA3 · the same entry in another collection · chain A against A, TM-score 1.00
  • O53333 · AlphaFold monomer V2.0 prediction for putative antitoxin HIGA3 (O53333) · a predicted model of the same protein · chain A against A, TM-score 0.73

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