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Crystal structure of dest bound to descb promoter and oleoyl-CoA

Analyse Crystal structure of dest bound to descb promoter and oleoyl-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3LSP
Type
protein + DNA
Length
240 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Dest; DNA (5'- D(*TP*TP*AP*CP*AP*TP*CP*AP*GP*TP*GP*AP*AP*CP*GP*CP*TP*TP*GP*TP*TP*GP*…
UniProt
Q9HUS3
Ligands
OLA, SO4
Pockets
1 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADestprotein19478% helix, 0% strandQ9HUS3
BDNA (5'- D(*TP*TP*AP*CP*AP*TP*CP*AP*GP*TP*GP*AP*AP*CP*GP*CP*TP*TP*GP*TP*TP*GP* AP*CP*TP*CP*GP*AP*TP*TP*G)-3')dna23——
DDNA (5'- D(*TP*CP*AP*AP*TP*CP*GP*AP*GP*TP*CP*AP*AP*CP*AP*AP*GP*CP*GP*TP*TP*CP* AP*CP*TP*GP*AP*TP*GP*TP*A)-3')dna23——

Ligands and binding sites

  • OLA · Oleic acid · ligand · chains A
  • SO4 · Sulfate ion · ion · 2 copies · chains A

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
13560.800.8934OLA

Interfaces

3 interfaces between chains.

  • B–D · 1780 Ų buried · 851 hydrogen bonds · nucleic-nucleic
  • A–B · 430 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–D · 426 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 3LSP · Crystal Structure of DesT bound to desCB promoter and oleoyl-CoA · the same entry in another collection · chain A against A, TM-score 1.00

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