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RNA/DNA dodecamer R(G)D(CGTATACGC) with magnesium binding sites

Analyse RNA/DNA dodecamer R(G)D(CGTATACGC) with magnesium binding sites in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DNX
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA (5'-R(*GP)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3')
Ligands: MG
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA/RNA (5'-R(GP)-D(CPGPTPAPTPAPCPGPC)-3')	dna	10	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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	126	0.35	0.72	12	MG

Interfaces

1 interface between chains.

A–B · 495 Å² buried · 40 hydrogen bonds · nucleic-nucleic

Compared structures

1DNX · RNA/DNA dodecamer R(G)D(CGTATACGC) with magnesium binding sites · 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 1DNX · PDBe 1DNX

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