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DNA holliday junction stabilized by fluorine halogen bond. F2J construct of related reference.

Analyse DNA holliday junction stabilized by fluorine halogen bond. F2J construct of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4GSI
Type
DNA
Length
80 nucleotides
Chains
8
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3'); DNA…
Pockets
2 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, C, F, HDNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3')dna10——
B, D, E, GDNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')dna10——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12450.490.7542empty
22350.460.7446empty

Interfaces

28 interfaces between chains.

  • A–E · 1001 Ų buried · 414 hydrogen bonds · nucleic-nucleic
  • C–G · 930 Ų buried · 387 hydrogen bonds · nucleic-nucleic
  • B–F · 800 Ų buried · 348 hydrogen bonds · nucleic-nucleic
  • D–H · 777 Ų buried · 383 hydrogen bonds · nucleic-nucleic
  • C–H · 313 Ų buried · 27 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 4GSI · DNA Holliday junction stabilized by fluorine halogen bond. F2J construct of related… · the same entry in another collection · chain A against A, TM-score 1.00

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