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The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites

Analyse The structure of an RNA dodecamer shows how tandem U-U base pairs increase the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 280D
Type: RNA
Length: 48 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP*C)-3')
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(GPGPCPGPCPUPUPGPCPGPUPC)-3')	rna	12	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	319	0.52	0.75	22	empty
2	280	0.48	0.74	20	empty

Interfaces

2 interfaces between chains.

A–B · 603 Å² buried · 70 hydrogen bonds · nucleic-nucleic
C–D · 588 Å² buried · 68 hydrogen bonds · nucleic-nucleic

Compared structures

280D · The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of… · the same entry in another collection · chain B against B, 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 280D · PDBe 280D

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