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MolNFT v1 · #7848 · DNA

CO(III)-bleomycin-ooh bound to an oligonucleotide containing a phosphoglycolate lesion

1GJ2 · 5'-D(*CP*CP*AP*AP*AP*G)-3': “CO(III)-bleomycin-ooh bound to an oligonucleotide containing a phosphoglycolate lesion”. Solution nmr, 5 ligands (PGA, BLB, PEO). MolNFT v1 #7848 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
1GJ2
Type
DNA
Length
25 nucleotides
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*CP*CP*AP*AP*AP*G)-3'; 5'-D(P*AP*CP*TP*GP*GP*G)-3'…
Ligands
PGA, BLB, PEO, 3CO, O

Structure

solution nmr · 3 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-D(*CP*CP*AP*AP*AP*G)-3'dna6——
B5'-D(P*AP*CP*TP*GP*GP*G)-3'dna6——
C5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'dna13——

Ligands and binding sites

  • PGA · 2-phosphoglycolic acid · ligand · chains A
  • BLB · Bleomycin B2 · ligand · chains A, B, C
  • PEO · Hydrogen peroxide · ligand · chains C
  • 3CO · Cobalt (III) ion · metal
  • O · Oxygen atom · ion · chains B

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

Interfaces

2 interfaces between chains.

  • A–C · 321 Ų buried · 29 hydrogen bonds · nucleic-nucleic
  • B–C · 292 Ų buried · 31 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 1GJ2 · CO(III)-bleomycin-ooh bound to an oligonucleotide containing a phosphoglycolate lesion · the same entry in another collection · chain B against B, TM-score 1.00

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