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Self-assembly of a 3D DNA crystal lattice (4X5 junction version) containing the J32 immobile holliday junction

Analyse Self-assembly of a 3D DNA crystal lattice (4X5 junction version) containing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6XGJ
Type
DNA
Length
42 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*AP*G)-3'); DNA…
Ligands
CAC

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*AP*G)-3')dna11——
BDNA (5'-D(P*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')dna10——
CDNA (5'-D(P*CP*TP*TP*GP*T)-3')dna5——
DDNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*AP*GP*TP*CP*TP*GP*C)- 3')dna16——

Ligands and binding sites

  • CAC · Cacodylate ion · metal · 3 copies · chains C, D

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

Interfaces

5 interfaces between chains.

  • A–D · 342 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • B–D · 334 Ų buried · 26 hydrogen bonds · nucleic-nucleic
  • C–D · 247 Ų buried · 6 hydrogen bonds · nucleic-nucleic
  • B–C · 145 Ų buried · 13 hydrogen bonds · nucleic-nucleic
  • A–C · 95 Ų buried · 9 hydrogen bonds · nucleic-nucleic

Compared structures

  • 6XGJ · Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J32… · the same entry in another collection · chain A against A, TM-score 1.00

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