MolNFT v1 · #103481 · RNA

Functional conservation despite structural divergence in ligand- responsive RNA switches

4PHY · RNA (26-mer): “Functional conservation despite structural divergence in ligand- responsive RNA switches”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.59). MolNFT v1 #103481 on GenesisL1: 3D structure, binding…

PDB: 4PHY
Type: RNA
Length: 46 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (26-mer); RNA (5'- R(*GP*CP*AP*GP*GP*AP*AP*CP*CP*GP*AP*GP*AP*GP*GP*CP*AP*CP*GP*C)-3')
Ligands: MG
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (26-mer)	rna	26	—	—
B	RNA (5'- R(GPCPAPGPGPAPAPCPCPGPAPGPAPGPGPCPAPCPGPC)-3')	rna	20	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A, B

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

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	504	0.59	0.74	27	ACT

Interfaces

1 interface between chains.

A–B · 999 Å² buried · 106 hydrogen bonds · nucleic-nucleic

Compared structures

4PHY · Functional conservation despite structural divergence in ligand-responsive RNA switches · 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 4PHY · PDBe 4PHY

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