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Solution structure of mithramycin dimers bound to partially overlapping sites on DNA

Analyse Solution structure of mithramycin dimers bound to partially overlapping sites… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
207D
Type
DNA
Length
20 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*TP*AP*GP*CP*TP*AP*GP*CP*TP*A)-3')
Ligands
DDA, DDL, MDA, CRH, MG

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(*TP*AP*GP*CP*TP*AP*GP*CP*TP*A)-3')dna10——

Ligands and binding sites

  • DDA · beta-D-Olivopyranose · ligand · 12 copies · chains A, B
  • DDL · 2,6-dideoxy-beta-D-galactopyranose · ligand · 4 copies · chains A, B
  • MDA · 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose · ligand · 4 copies · chains A, B
  • CRH · 1,2-hydro-1-oxy-3,4-hydro-3-(1-methoxy-2-oxy-3,4-dihydroxypentyl)-8,9-dihyroxy-7-methylanthracene · ligand · 4 copies · chains A, B
  • MG · Magnesium ion · metal · 2 copies · 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 · 444 Ų buried · 60 hydrogen bonds · nucleic-nucleic

Compared structures

  • 207D · Solution structure of mithramycin dimers bound to partially overlapping sites on DNA · the same entry in another collection · chain A against A, TM-score 1.00

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