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Sequence specific recognition of RNA hairpins by the SAM domain of VTS1

Analyse Sequence specific recognition of RNA hairpins by the SAM domain of VTS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F8K
Type: protein + RNA
Length: 99 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*UP*AP*AP*UP*CP*UP*UP*UP*GP*AP*CP*AP*GP*AP*UP*U)-3'; Protein VTS1
UniProt: Q08831
Pockets: 1 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-R(UPAPAPUPCPUPUPUPGPAPCPAPGPAPUPU)-3'	rna	15	—	—
A	Protein VTS1	protein	84	64% helix, 0% strand	Q08831

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.51	0.84	17	empty

Interfaces

1 interface between chains.

B–A · 472 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

2F8K · Sequence specific recognition of RNA hairpins by the SAM domain of Vts1 · the same entry in another collection · chain B against B, TM-score 1.00
Q08831 · AlphaFold monomer V2.0 prediction for RNA-binding protein VTS1 (Q08831) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q08831
Elsewhere: RCSB PDB 2F8K · PDBe 2F8K · UniProt Q08831

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