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Interactions of an echinomycin-DNA complex with MANGANESE(II) ions

Analyse Interactions of an echinomycin-DNA complex with MANGANESE(II) ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3GO3
Type
protein + DNA
Length
32 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'; Echinomycin
Ligands
QUI, MN

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'dna8——
C, DEchinomycinprotein80% helix, 0% strand—

Ligands and binding sites

  • QUI · 2-carboxyquinoxaline · ligand · 4 copies · chains A, B, C, D
  • MN · Manganese (II) ion · metal · 2 copies · chains A, B
  • PEG · Di(hydroxyethyl)ether · additive · chains A, B

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

Interfaces

5 interfaces between chains.

  • A–B · 377 Ų buried · 25 hydrogen bonds · nucleic-nucleic
  • B–D · 241 Ų buried · 4 hydrogen bonds · protein-nucleic
  • A–C · 235 Ų buried · 4 hydrogen bonds · protein-nucleic
  • B–C · 230 Ų buried · 3 hydrogen bonds · protein-nucleic
  • A–D · 221 Ų buried · 4 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

  • 3GO3 · Interactions of an echinomycin-DNA complex with manganese(II) ions · the same entry in another collection · chain A against A, TM-score 1.00

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