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Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version) containing the J16 immobile holliday junction with R3 symmetry

Analyse Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7JLA
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*AP*CP*GP*AP*CP*AP*GP*TP*GP*AP*CP*GP*CP*CP*GP*AP*CP*TP*C)- 3'); DNA…
Ligands
CAC

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'- D(*GP*AP*AP*CP*GP*AP*CP*AP*GP*TP*GP*AP*CP*GP*CP*CP*GP*AP*CP*TP*C)- 3')dna21——
CDNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*G)-3')dna8——
DDNA (5'-D(P*CP*TP*GP*TP*CP*GP*T)-3')dna7——
ADNA (5'-D(P*GP*CP*GP*TP*CP*A)-3')dna6——

Ligands and binding sites

  • CAC · Cacodylate ion · metal · 2 copies · chains C, A

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

Interfaces

5 interfaces between chains.

  • B–D · 339 Ų buried · 34 hydrogen bonds · nucleic-nucleic
  • B–A · 303 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • B–C · 276 Ų buried · 30 hydrogen bonds · nucleic-nucleic
  • C–A · 104 Ų buried · 4 hydrogen bonds · nucleic-nucleic
  • D–A · 101 Ų buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

  • 7JLA · Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the… · the same entry in another collection · chain B against B, TM-score 1.00

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