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MolNFT v1 · #178850 · DNA

Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version) containing the J36 immobile holliday junction with R3 symmetry

7JNM · DNA (5'- D(*GP*AP*AP*CP*GP*AP*CP*AP*GP*TP*GP*AP*CP*GP*AP*CP*…: “Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version) containing the J36 immobile holliday…”. X-ray diffraction, 1 ligand (CAC). MolNFT v1 #178850 on…

PDB
7JNM
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*AP*CP*GP*AP*GP*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*AP*CP*GP*AP*GP*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*TP*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 · 33 hydrogen bonds · nucleic-nucleic
  • B–C · 290 Ų buried · 29 hydrogen bonds · nucleic-nucleic
  • B–A · 286 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • C–A · 105 Ų buried · 4 hydrogen bonds · nucleic-nucleic
  • D–A · 99 Ų buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

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

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