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Crystal structure of double-stranded DNA agggatccct in complex with ZN2+

Analyse Crystal structure of double-stranded DNA agggatccct in complex with ZN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DY5
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*GP*GP*GP*AP*TP*CP*CP*CP*T)-3')
Ligands: SPD, ZN

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(APGPGPGPAPTPCPCPCPT)-3')	dna	10	—	—

Ligands and binding sites

SPD · Spermidine · ligand · chains A
ZN · Zinc ion · metal · 3 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 · 479 Å² buried · 43 hydrogen bonds · nucleic-nucleic

Compared structures

6DY5 · Crystal structure of double-stranded DNA AGGGATCCCT in complex with Zn2+ · 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 6DY5 · PDBe 6DY5

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