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MolNFT v1 · #5520 · DNA

Average solution structure of D(TTGGCCAA)2 bound to chromomycin-A3 and cobalt

1EKI · DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3'): “Average solution structure of D(TTGGCCAA)2 bound to chromomycin-A3 and cobalt”. Solution nmr, 6 ligands (DDA, 2GL, 1GL). MolNFT v1 #5520 on GenesisL1: 3D structure, binding sites and pockets…

PDB
1EKI
Type
DNA
Length
16 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')
Ligands
DDA, 2GL, 1GL, ERI, CPH, CO

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')dna8——

Ligands and binding sites

  • DDA · beta-D-Olivopyranose · ligand · 4 copies · chains B, A
  • 2GL · 4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose · ligand · 2 copies · chains A, B
  • 1GL · 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose · ligand · 2 copies · chains A, B
  • ERI · 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose · ligand · 2 copies · chains A, B
  • CPH · (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose · ligand · 2 copies · chains A, B
  • CO · Cobalt (II) ion · metal · 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 · 376 Ų buried · 35 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1EKI · Average solution structure of D(TTGGCCAA)2 bound to chromomycin-A3 and cobalt · the same entry in another collection · chain A against A, TM-score 1.00

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