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MolNFT v1 · #178746 · DNA

Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version) containing the J2 immobile holliday junction

7JKE · DNA (5'- D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*TP*GP*AP*CP*GP*AP*GP*…: “Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version) containing the J2 immobile holliday…”. X-ray diffraction, 2 ligands (MG, CAC). MolNFT v1 #178746…

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

Structure

x-ray diffraction · 4 distinct chains.

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

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains A, B
  • CAC · Cacodylate ion · metal · chains A, B

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

Interfaces

5 interfaces between chains.

  • A–D · 335 Ų buried · 27 hydrogen bonds · nucleic-nucleic
  • A–C · 298 Ų buried · 31 hydrogen bonds · nucleic-nucleic
  • A–B · 286 Ų buried · 26 hydrogen bonds · nucleic-nucleic
  • B–D · 98 Ų buried · 2 hydrogen bonds · nucleic-nucleic
  • B–C · 93 Ų buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

  • 7JKE · Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J2… · the same entry in another collection · chain A against A, TM-score 1.00

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