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MolNFT v1 · #31451 · DNA

G4(BR)UTTG4 dimeric quadruplex

2AVJ · 5'-D(*GP*GP*GP*GP*(BRU)P*TP*TP*GP*GP*GP*G)-3': “G4(BR)UTTG4 dimeric quadruplex”. X-ray diffraction, 2 ligands (K, CAC), 1 pocket (best druggability 0.26). MolNFT v1 #31451 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
2AVJ
Type
DNA
Length
66 nucleotides
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*GP*GP*GP*(BRU)P*TP*TP*GP*GP*GP*G)-3'
Ligands
K, CAC
Pockets
1 · best druggability 0.26

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, F5'-D(*GP*GP*GP*GP*(BRU)P*TP*TP*GP*GP*GP*G)-3'dna11——

Ligands and binding sites

  • K · Potassium ion · metal · 14 copies · chains A, B, C, D, E, F
  • CAC · Cacodylate ion · metal · 2 copies · chains D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1560.260.7411empty

Interfaces

7 interfaces between chains.

  • A–B · 518 Ų buried · 38 hydrogen bonds · nucleic-nucleic
  • C–D · 416 Ų buried · 36 hydrogen bonds · nucleic-nucleic
  • E–F · 401 Ų buried · 36 hydrogen bonds · nucleic-nucleic
  • C–F · 246 Ų buried · 4 hydrogen bonds · nucleic-nucleic
  • D–E · 203 Ų buried · 6 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

  • 2AVJ · G4(Br)UTTG4 dimeric quadruplex · the same entry in another collection · chain A against A, TM-score 1.00

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