Research workbench

Base pairing and structure insights into the 5-formylcytosine in RNA duplex

Analyse Base pairing and structure insights into the 5-formylcytosine in RNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HNQ
Type: RNA
Length: 104 nucleotides
Chains: 13
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5FC modified RNA
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M	5FC modified RNA	rna	8	—	—

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	183	0.38	0.72	21	empty
2	66	0.28	0.74	10	empty

Interfaces

25 interfaces between chains.

C–D · 380 Å² buried · 40 hydrogen bonds · nucleic-nucleic
E–F · 379 Å² buried · 38 hydrogen bonds · nucleic-nucleic
A–B · 375 Å² buried · 33 hydrogen bonds · nucleic-nucleic
I–J · 373 Å² buried · 36 hydrogen bonds · nucleic-nucleic
K–L · 369 Å² buried · 35 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 13 modified (nucleotide modification).

Compared structures

5HNQ · Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex · 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 5HNQ · PDBe 5HNQ

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