MolNFT v1 · #137876 · DNA

Crystal structure of inosine-substituted duplex DNA

5W20 · DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*TP*GP*G)-3'): “Crystal structure of inosine-substituted duplex DNA”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.24). MolNFT v1 #137876 on GenesisL1: 3D structure, binding sites…

PDB: 5W20
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*TP*GP*G)-3')
Ligands: MG
Pockets: 1 · best druggability 0.24

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

MG · Magnesium ion · metal · 6 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	51	0.24	0.73	12	MG

Interfaces

1 interface between chains.

A–B · 464 Å² buried · 38 hydrogen bonds · nucleic-nucleic

Compared structures

5W20 · Crystal Structure of inosine-substituted duplex DNA · 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 5W20 · PDBe 5W20

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