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MolNFT v1 · #178639 · DNA

Self-assembly of a 3D DNA crystal lattice (4X6 junction version) containing the J22 immobile holliday junction

7JH9 · DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*A)-3'): “Self-assembly of a 3D DNA crystal lattice (4X6 junction version) containing the J22 immobile holliday junction”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability…

PDB
7JH9
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*CP*TP*GP*A)-3'); DNA…
Ligands
MG
Pockets
1 · best druggability 0.22

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*A)-3')dna12——
BDNA (5'-D(P*CP*GP*GP*CP*AP*CP*TP*CP*A)-3')dna9——
CDNA (5'-D(P*TP*CP*AP*CP*CP*G)-3')dna6——
DDNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*GP*TP*CP*TP*GP*C)- 3')dna15——

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1510.220.7210empty

Interfaces

6 interfaces between chains.

  • A–D · 344 Ų buried · 31 hydrogen bonds · nucleic-nucleic
  • B–D · 288 Ų buried · 23 hydrogen bonds · nucleic-nucleic
  • C–D · 247 Ų buried · 7 hydrogen bonds · nucleic-nucleic
  • B–C · 149 Ų buried · 13 hydrogen bonds · nucleic-nucleic
  • A–C · 127 Ų buried · 9 hydrogen bonds · nucleic-nucleic

Compared structures

  • 7JH9 · Self-assembly of a 3D DNA crystal lattice (4x6 junction version) containing the J22… · the same entry in another collection · chain A against A, TM-score 1.00

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