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Crystal structure of echinomycin-D(ACGACGT/ACGTCGT) complex

Analyse Crystal structure of echinomycin-D(ACGACGT/ACGTCGT) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5YTY
Type
protein + DNA
Length
30 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3'); DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3'); Echinomycin
Ligands
QUI, MG, MN

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3')dna7——
BDNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3')dna7——
D, FEchinomycinprotein80% helix, 0% strand—

Ligands and binding sites

  • QUI · 2-carboxyquinoxaline · ligand · 4 copies · chains A, B, D, F
  • MG · Magnesium ion · metal · 2 copies · chains A, B
  • MN · Manganese (II) ion · metal · chains B

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

Interfaces

6 interfaces between chains.

  • A–B · 349 Ų buried · 26 hydrogen bonds · nucleic-nucleic
  • A–D · 218 Ų buried · 3 hydrogen bonds · protein-nucleic
  • B–F · 208 Ų buried · 3 hydrogen bonds · protein-nucleic
  • A–F · 207 Ų buried · 4 hydrogen bonds · protein-nucleic
  • B–D · 192 Ų buried · 3 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 modified, 4 covalent, 4 d-amino (covalent ligand, D-amino acid, methylation, nonstandard).

Compared structures

  • 5YTY · Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex · the same entry in another collection · chain F against F, TM-score 1.00

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