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MolNFT v1 · #165709 · DNA

Crystal structure of a self-assembling DNA crystal scaffold with rhombohedral symmetry

6U40 · DNA (5'- D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*…: “Crystal structure of a self-assembling DNA crystal scaffold with rhombohedral symmetry”. X-ray diffraction, 1 ligand (CAC). MolNFT v1 #165709 on GenesisL1: 3D…

PDB
6U40
Type
DNA
Length
42 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)- 3'); DNA…
Ligands
CAC

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'- D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)- 3')dna21——
ADNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')dna7——
CDNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')dna9——
DDNA (5'-D(P*GP*TP*CP*AP*G)-3')dna5——

Ligands and binding sites

  • CAC · Cacodylate ion · metal · 2 copies · chains A, D

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

Interfaces

5 interfaces between chains.

  • B–A · 338 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • B–C · 338 Ų buried · 25 hydrogen bonds · nucleic-nucleic
  • B–D · 258 Ų buried · 23 hydrogen bonds · nucleic-nucleic
  • A–C · 107 Ų buried · 3 hydrogen bonds · nucleic-nucleic
  • A–D · 103 Ų buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

  • 6U40 · Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry · the same entry in another collection · chain B against B, TM-score 1.00

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