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Structure of the DNA-binding domain of lux arrhythmo

Analyse Structure of the DNA-binding domain of lux arrhythmo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5LXU
Type
protein + DNA
Length
77 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Transcription factor lux; DNA (5'- D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*G…
UniProt
Q9SNB4
Pockets
1 · best druggability 0.30

Structure

x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATranscription factor luxprotein5763% helix, 0% strandQ9SNB4
UDNA (5'- D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')dna10——
BDNA (5'- D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')dna10——

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1540.300.7611empty

Interfaces

3 interfaces between chains.

  • U–B · 431 Ų buried · 39 hydrogen bonds · nucleic-nucleic
  • A–B · 389 Ų buried · 10 hydrogen bonds · protein-nucleic
  • A–U · 354 Ų buried · 8 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

  • 5LXU · Structure of the DNA-binding domain of LUX ARRHYTHMO · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9SNB4 · AlphaFold monomer V2.0 prediction for transcription factor lux (Q9SNB4) · a predicted model of the same protein · chain A against A, TM-score 0.93

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