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Crystal structure of a biotin-binding RNA pseudoknot

Analyse Crystal structure of a biotin-binding RNA pseudoknot in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F27
Type: RNA
Length: 30 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(*AP*CP*CP*GP*UP*CP*AP*GP*AP*GP*GP*AP*CP*AP*CP*GP*GP*UP*U) -3'); RNA…
Ligands: BTN, MG
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'- R(APCPCPGPUPCPAPGPAPGPGPAPCPAPCPGPGPUP*U) -3')	rna	19	—	—
B	RNA (5'-R(APAPAPAPAPGPUPCPCPUP*C)-3')	rna	11	—	—

Ligands and binding sites

BTN · Biotin · ligand · chains A, B
MG · Magnesium ion · metal · 6 copies · chains A, B

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

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	0.37	0.79	8	BTN, MG
2	103	0.34	0.74	12	MG

Interfaces

1 interface between chains.

A–B · 818 Å² buried · 51 hydrogen bonds · nucleic-nucleic

Compared structures

1F27 · Crystal structure of a biotin-binding RNA pseudoknot · 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 1F27 · PDBe 1F27

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