MolNFT v2 · #215358 · DNA

Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for 5 minutes

8OE7 · DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'): “Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide…”. X-ray diffraction at 1.25, 2 ligands (PEO, CU), 1 pocket (best druggability 0.48).…

PDB: 8OE7
Type: DNA
Length: 48 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.25
Molecule: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
Ligands: PEO, CU
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · resolution 1.25 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	DNA (5'-D(CPGPCPGPCPG)-3')	dna	6	—	—

Ligands and binding sites

PEO · Hydrogen peroxide · ligand · 7 copies · chains A, B, G, H, C
CU · Copper (II) ion · metal · 20 copies · chains A, B, D, C, E, F, H, G

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.48	0.75	25	CU, PEO

Interfaces

10 interfaces between chains.

E–F · 328 Å² buried · 21 hydrogen bonds · nucleic-nucleic
A–B · 328 Å² buried · 24 hydrogen bonds · nucleic-nucleic
G–H · 326 Å² buried · 21 hydrogen bonds · nucleic-nucleic
C–D · 326 Å² buried · 20 hydrogen bonds · nucleic-nucleic
B–D · 109 Å² buried · 1 hydrogen bond · nucleic-nucleic

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8OE7 · PDBe 8OE7

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