MolNFT v1 · #21725 · DNA

A duplex DNA with an abasic site in a da tract, alpha form, NMR, minimized average structure

1SJK · DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3'): “A duplex DNA with an abasic site in a da tract, alpha form, NMR, minimized average structure”. Solution nmr, 1 ligand (ORP), 1 pocket (best druggability 0.30). MolNFT v1 #21725 on…

PDB: 1SJK
Type: DNA
Length: 23 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3'); DNA…
Ligands: ORP
Pockets: 1 · best druggability 0.30

Structure

solution nmr · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(CPGPCPAPAPAPAPAPTPGPCPG)-3')	dna	12	—	—
B	DNA (5'-D(CPGPCPAPTPTPORPPTPTPGPCPG)-3')	dna	11	—	—

Ligands and binding sites

ORP · 2-deoxy-5-phosphono-ribose · ligand · 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	50	0.30	0.77	11	empty

Interfaces

1 interface between chains.

A–B · 627 Å² buried · 61 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1SJK · A duplex DNA with an abasic site in a da tract, alpha form, NMR, minimized average… · 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 1SJK · PDBe 1SJK

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