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Structure determination of a self-assembling DNA crystal

Analyse Structure determination of a self-assembling DNA crystal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5KEO
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*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)- 3'); DNA…
Ligands
CAC

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'- D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)- 3')dna21——
BDNA (5'-D(P*CP*GP*TP*CP*A)-3')dna5——
CDNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')dna9——
DDNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')dna7——

Ligands and binding sites

  • CAC · Cacodylate ion · metal · 2 copies · chains 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
  • A–C · 334 Ų buried · 25 hydrogen bonds · nucleic-nucleic
  • A–B · 255 Ų buried · 22 hydrogen bonds · nucleic-nucleic
  • B–D · 104 Ų buried · 2 hydrogen bonds · nucleic-nucleic
  • B–C · 96 Ų buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5KEO · Structure Determination of a Self-Assembling DNA Crystal · the same entry in another collection · chain A against A, TM-score 1.00

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