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1.5 a resolution structure of a synthetic DNA hairpin with a stilbenediether linker

Analyse 1.5 a resolution structure of a synthetic DNA hairpin with a stilbenediether… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PUY
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)- 3'
Ligands: S02, MG
Pockets: 1 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(GPTPTPTPTPGP(S02)PCPAPAPAPAP*C)- 3'	dna	12	—	—

Ligands and binding sites

S02 · Phosphoric acid mono-[2-(4-{2-[4-(2-hydroxy-ethoxy)-cyclohexylidene]-ethylidene}-cyclohexyloxy) -ethyl] ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 5 copies · chains A, B

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	142	0.45	0.77	14	MG

Interfaces

1 interface between chains.

A–B · 79 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1PUY · 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker · 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 1PUY · PDBe 1PUY

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