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NMR study of deoxyribonucleic acid complexed with actinomycin D

Analyse NMR study of deoxyribonucleic acid complexed with actinomycin D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1FJA
Type
protein + DNA
Length
32 residues
Chains
4
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*AP*AP*GP*CP*GP*CP*TP*T)-3'); Actinomycin D
Ligands
PXZ

Structure

solution nmr · 2 distinct chains · 0% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(*AP*AP*GP*CP*GP*CP*TP*T)-3')dna6——
C, DActinomycin Dprotein100% helix, 20% strand—

Ligands and binding sites

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

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

Interfaces

6 interfaces between chains.

  • A–B · 285 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • B–C · 226 Ų buried · 3 hydrogen bonds · protein-nucleic
  • A–D · 225 Ų buried · 3 hydrogen bonds · protein-nucleic
  • A–C · 217 Ų buried · 2 hydrogen bonds · protein-nucleic
  • B–D · 215 Ų buried · 2 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 1FJA · NMR study of deoxyribonucleic acid complexed with actinomycin D · the same entry in another collection · chain A against A, TM-score 1.00

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