Research workbench

RhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine

Analyse RhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 9BUN
Type: RNA
Length: 192 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.1
Molecule: RNA (48-mer)
Ligands: IRI, FH8
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · resolution 2.1 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (48-mer)	rna	48	—	—

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 15 copies · chains A, B, C, D
FH8 · 5-carboxy methylrhodamine · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	721	0.64	0.75	39	IRI
2	398	0.58	0.76	24	IRI
3	349	0.58	0.77	18	IRI
4	402	0.56	0.75	24	IRI
5	332	0.54	0.75	27	IRI

Interfaces

5 interfaces between chains.

A–D · 355 Å² buried · 22 hydrogen bonds · nucleic-nucleic
A–C · 279 Å² buried · 9 hydrogen bonds · nucleic-nucleic
B–C · 141 Å² buried · 0 hydrogen bonds · nucleic-nucleic
A–B · 138 Å² buried · 1 hydrogen bond · nucleic-nucleic
C–D · 17 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 9BUN · PDBe 9BUN

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