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MolNFT v1 · #178731 · DNA

Self-assembly of a 3D DNA crystal lattice (4X6 scramble junction version) containing the J3 immobile holliday junction with R3 symmetry

7JJY · DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*GP*TP*GP*A)-3'): “Self-assembly of a 3D DNA crystal lattice (4X6 scramble junction version) containing the J3 immobile holliday…”. X-ray diffraction, 1 ligand (CAC). MolNFT v1 #178731 on GenesisL1…

PDB
7JJY
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*A)-3'); DNA…
Ligands
CAC

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*GP*TP*GP*A)-3')dna12——
BDNA (5'-D(P*CP*GP*TP*CP*GP*AP*CP*TP*C)-3')dna9——
CDNA (5'-D(P*TP*CP*AP*AP*CP*G)-3')dna6——
DDNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*CP*TP*GP*TP*CP*GP*T)- 3')dna15——

Ligands and binding sites

  • CAC · Cacodylate ion · metal · 2 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 · 344 Ų buried · 40 hydrogen bonds · nucleic-nucleic
  • B–D · 285 Ų buried · 29 hydrogen bonds · nucleic-nucleic
  • C–D · 263 Ų buried · 7 hydrogen bonds · nucleic-nucleic
  • B–C · 164 Ų buried · 16 hydrogen bonds · nucleic-nucleic
  • A–C · 154 Ų buried · 15 hydrogen bonds · nucleic-nucleic

Compared structures

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

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