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Self-complementary duplex DNA containing an internucleoside phosphoroselenolate

Analyse Self-complementary duplex DNA containing an internucleoside phosphoroselenolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6S7D
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*(XCI)P*CP*CP*CP*GP*GP*GP*AP*C)-3')
Ligands: SPM, BA, NA, CL
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

SPM · Spermine · ligand · chains A, B
BA · Barium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion

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	122	0.34	0.72	13	NA

Interfaces

1 interface between chains.

A–B · 474 Å² buried · 65 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

6S7D · Self-complementary duplex DNA containing an internucleoside phosphoroselenolate · 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 6S7D · PDBe 6S7D

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