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Multiple binding modes of anticancer drug actinomycin D: X-ray, molecular modeling, and spectroscopic studies of D(GAAGCTTC)2- actinomycin D complexes and its host DNA

Analyse Multiple binding modes of anticancer drug actinomycin D: X-ray, molecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
173D
Type
protein + DNA
Length
26 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3'); Actinomycin D
Ligands
PXZ

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')dna8——
C, DActinomycin Dprotein50% helix, 0% strand—

Ligands and binding sites

  • PXZ · 2-amino-1,9-dicarbonyl-4,6-dimethyl-10-dehydro-phenoxazin-3-one · ligand · 2 copies · chains A, C, B, D

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

Interfaces

2 interfaces between chains.

  • A–C · 148 Ų buried · 4 hydrogen bonds · protein-nucleic
  • B–D · 111 Ų buried · 3 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified, 2 covalent, 2 d-amino (methylation, covalent ligand, D-amino acid).

Compared structures

  • 173D · Multiple binding modes of anticancer drug actinomycin D: X-ray, molecular modeling, and… · the same entry in another collection · chain A against A, TM-score 1.00

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