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Crystal structure of a brominated RNA helix with four mismatched base pairs

Analyse Crystal structure of a brominated RNA helix with four mismatched base pairs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QBP
Type: RNA
Length: 84 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*UP*GP*(CBV)P*(CBV) P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	5'-R(UPGP(CBV)P(CBV) PAPGPUPUPCPGPCPUPGPGP*C)-3'	rna	14	—	—

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.57	0.74	26	empty
2	393	0.56	0.75	26	empty
3	300	0.51	0.75	24	empty
4	62	0.25	0.72	15	empty

Interfaces

11 interfaces between chains.

C–D · 660 Å² buried · 77 hydrogen bonds · nucleic-nucleic
E–F · 654 Å² buried · 78 hydrogen bonds · nucleic-nucleic
A–B · 649 Å² buried · 74 hydrogen bonds · nucleic-nucleic
A–C · 71 Å² buried · 0 hydrogen bonds · nucleic-nucleic
B–D · 70 Å² buried · 5 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 12 modified (nucleotide modification).

Compared structures

1QBP · Crystal structure of a brominated RNA helix with four mismatched base pairs · 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 1QBP · PDBe 1QBP

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