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MolNFT v1 · #162768 · DNA

Imidazole polyamide-DNA complex NMR structure (5'-cgatgtacatcg-3')

6RIO · DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'): “Imidazole polyamide-DNA complex NMR structure (5'-cgatgtacatcg-3')”. Solution nmr, 1 ligand (K4Z). MolNFT v1 #162768 on GenesisL1: 3D structure, binding sites and pockets…

PDB
6RIO
Type
DNA
Length
24 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')
Ligands
K4Z

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')dna12——

Ligands and binding sites

  • K4Z · 3-[3-[[4-[[4-[[4-[[4-[[(2~{R})-2-azaniumyl-4-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]butanoyl]amino]-1-methyl-imidazol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]propanoylamino]propyl-dimethyl-azanium · ligand · chains A, B

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

Interfaces

1 interface between chains.

  • A–B · 640 Ų buried · 50 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 6RIO · Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3') · the same entry in another collection · chain A against A, TM-score 1.00

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