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Crystal structure of echinomycin-(ACGTACGT)2 solved by sad

Analyse Crystal structure of echinomycin-(ACGTACGT)2 solved by sad in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2ADW
Type
protein + DNA
Length
64 residues
Chains
8
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, NI, ZN

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
A, C, E, G5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'dna8——
H, I, J, KEchinomycinprotein80% helix, 0% strand—

Ligands and binding sites

  • QUI · 2-carboxyquinoxaline · ligand · 8 copies · chains A, C, H, I, E, G, J, K
  • NI · Nickel (II) ion · metal · chains E
  • ZN · Zinc ion · metal · chains E
  • MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, C

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

Interfaces

14 interfaces between chains.

  • E–G · 380 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • A–C · 379 Ų buried · 27 hydrogen bonds · nucleic-nucleic
  • E–K · 241 Ų buried · 4 hydrogen bonds · protein-nucleic
  • C–H · 240 Ų buried · 5 hydrogen bonds · protein-nucleic
  • C–I · 239 Ų buried · 3 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 16 modified, 8 covalent, 8 d-amino (covalent ligand, D-amino acid, methylation, nonstandard).

Compared structures

  • 2ADW · Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD · the same entry in another collection · chain A against A, TM-score 1.00

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