GL1X · GenesisL1 explorer

Research workbench

Synthetic DNA hairpin with stilbenediether linker

Analyse Synthetic DNA hairpin with stilbenediether linker in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1CS7
Type
DNA
Length
48 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02) *CP*AP*AP*AP*AP*C)-3'
Ligands
S02, SR
Pockets
3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02) *CP*AP*AP*AP*AP*C)-3'dna12——

Ligands and binding sites

  • S02 · Phosphoric acid mono-[2-(4-{2-[4-(2-hydroxy-ethoxy)-cyclohexylidene]-ethylidene}-cyclohexyloxy) -ethyl] ester · ligand · 4 copies · chains A, B, C, D
  • SR · Strontium ion · metal · 4 copies · chains C, D

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
14870.570.7424S02, SR
2550.250.7312SR
3500.210.7111SR

Interfaces

4 interfaces between chains.

  • C–D · 54 Ų buried · 0 hydrogen bonds · nucleic-nucleic
  • B–C · 35 Ų buried · 0 hydrogen bonds · nucleic-nucleic
  • A–B · 31 Ų buried · 0 hydrogen bonds · nucleic-nucleic
  • A–D · 12 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 covalent, 4 modified (covalent ligand, nucleotide modification).

Compared structures

  • 1CS7 · Synthetic DNA hairpin with stilbenediether linker · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.