MolNFT v1 · #190598 · DNA

Crystal structure of DNA-AG(I) rod comprising a one-dimensional array of 11 silver ions

7XKM · DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3'): “Crystal structure of DNA-AG(I) rod comprising a one-dimensional array of 11 silver ions”. X-ray diffraction, 1 ligand (AG). MolNFT v1 #190598 on GenesisL1: 3D structure…

PDB: 7XKM
Type: DNA
Length: 48 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
Ligands: AG

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(CPGPCPGPCP(BRU)PCP(BRU)PCPGPCPG)-3')	dna	12	—	—

Ligands and binding sites

AG · Silver ion · metal · 23 copies · chains A, B, C, D

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

Interfaces

5 interfaces between chains.

A–B · 511 Å² buried · 22 hydrogen bonds · nucleic-nucleic
C–D · 489 Å² buried · 21 hydrogen bonds · nucleic-nucleic
B–C · 104 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–D · 98 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–C · 84 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

7XKM · Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7XKM · PDBe 7XKM

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