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MolNFT v1 · #57155 · DNA

High-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA dodecamer duplex

363D · 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)…: “High-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA dodecamer duplex”. X-ray diffraction, 6 ligands (C42, G38, A43). MolNFT v1 #57155 on…

PDB
363D
Type
DNA
Length
6 nucleotides
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM) P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
Ligands
C42, G38, A43, NYM, NH4, CL

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, F5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM) P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'dna1——

Ligands and binding sites

  • C42 · 3'-amino-2'-deoxy-cytidine-5'-monophosphate · ligand · 24 copies · chains B, C, A, F, D, E
  • G38 · 3'-amino-2'-deoxy-guanosine-5'-monophosphate · ligand · 18 copies · chains B, A, D, C, F, E
  • A43 · 3'-amino deoxyadenosine 5'-monophosphate · ligand · 12 copies
  • NYM · 3'-deoxy-3'-aminothymidine monophosphate · ligand · 12 copies
  • NH4 · Ammonium ion · ion · 24 copies · chains F
  • CL · Chloride ion · ion · 12 copies · chains F

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

Interfaces

2 interfaces between chains.

  • A–F · 33 Ų buried · 0 hydrogen bonds · nucleic-nucleic
  • B–C · 32 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

  • 363D · High-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA… · the same entry in another collection · chain A against A, TM-score 1.00

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