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MolNFT v1 · #101908 · DNA

O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine

4O5W · DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'): “O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine”. X-ray diffraction, 3 ligands (HT, MG, SR), 1 pocket (best…

PDB
4O5W
Type
DNA
Length
24 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3')
Ligands
HT, MG, SR
Pockets
1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3')dna12——

Ligands and binding sites

  • HT · 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-benzimidazole · ligand · chains A, B
  • MG · Magnesium ion · metal · 2 copies · chains A, B
  • SR · Strontium ion · metal · chains B

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
1610.270.7415HT

Interfaces

1 interface between chains.

  • A–B · 595 Ų buried · 49 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 4O5W · O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair… · the same entry in another collection · chain A against A, TM-score 1.00

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