MolNFT v1 · #27811 · DNA

Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogs

1XUX · DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3'): “Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry…”. X-ray diffraction, 2 pockets (best druggability 0.26). MolNFT v1 #27811…

PDB: 1XUX
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
Pockets: 2 · best druggability 0.26

Structure

x-ray diffraction · 1 distinct chain.

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.26	0.72	11	empty
2	53	0.22	0.71	12	empty

Interfaces

6 interfaces between chains.

C–D · 499 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–B · 482 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–C · 147 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–D · 122 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 121 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

1XUX · Structural rationalization of a large difference in RNA affinity despite a small… · 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 1XUX · PDBe 1XUX

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