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Crystal structure of DNA duplex containing 4-thiothymine-2AG(I)-4- thiothymine base pairs

Analyse Crystal structure of DNA duplex containing 4-thiothymine-2AG(I)-4- thiothymine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XUV
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*GP*AP*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3')
Ligands: AG, K

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(CPGPCPGPAP(8RO)P(8RO)PTPCPGPCPG)-3')	dna	12	—	—

Ligands and binding sites

AG · Silver ion · metal · 4 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B

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

Interfaces

1 interface between chains.

A–B · 574 Å² buried · 47 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

5XUV · Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4-thiothymine base pairs · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5XUV · PDBe 5XUV

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