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Im polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies

Analyse Im polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5OE1
Type
DNA
Length
24 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
Ligands
PYB, 9TK, ABU, IMT, 9T8

Structure

solution nmr · 1 distinct chain.

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

Ligands and binding sites

  • PYB · 4-amino-(1-methylpyrrole)-2-carboxylic acid · ligand · 6 copies · chains A, B
  • 9TK · 1-methylimidazole-2-carboxylic acid · ligand · chains A
  • ABU · Gamma-amino-butanoic acid · ligand · chains A, B
  • IMT · 4-amino-(1-methylimidazole)-2-carboxylic acid · ligand · chains B
  • 9T8 · 3-(3-azaniumylpropanoylamino)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 · 507 Ų buried · 42 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 5OE1 · Im polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies · the same entry in another collection · chain A against A, TM-score 1.00

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