› 8xpb

X-ray diffraction
2Å resolution

Crystal structure of d(ACGCCGT/ACGGCGT) in complex with Echinomycin

Released:
DOI: 10.2210/pdb8xpb/pdb
PDB entry 8xpb coloured by chain, front view.
PDB entry 8xpb coloured by chain, side view.
PDB entry 8xpb coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.
Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH
Nucleic Acids Res (2024)
PMID: 38989613

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-244746 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Echinomycin Chains: D, E
Molecule details ›
Chains: D, E
Length: 8 amino acids
Theoretical weight: 809 Da
Source organism: Streptomyces echinatus
DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*CP*GP*CP*CP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 7 nucleotides
Theoretical weight: 2.1 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 3 x MN
Ligand QUI 4 x QUI
2 modified residues:
Ligand DSN 4 x DSN
Ligand MVA 4 x MVA

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P3112
Unit cell:
a: 46.317Å b: 46.317Å c: 47.971Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.211 0.216
Expression system: Not provided

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