MolNFT v1 · #103195 · RNA

Functional conservation despite structural divergence in ligand- responsive RNA switches

4P97 · RNA (5'-R(*CP*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*C)…: “Functional conservation despite structural divergence in ligand- responsive RNA switches”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.30). MolNFT v1…

PDB: 4P97
Type: RNA
Length: 54 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*CP*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*C)- 3'); RNA…
Ligands: CA
Pockets: 2 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RNA (5'-R(CPGPUPCPUPAPCPCPCPAPCPCPUPCPGPC)- 3')	rna	16	—	—
B, D	RNA (5'-R(CPGPAPGPAPGPGPAPCPGP*G)-3')	rna	11	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, C

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	78	0.30	0.74	11	empty
2	62	0.26	0.73	10	empty

Interfaces

2 interfaces between chains.

C–D · 608 Å² buried · 54 hydrogen bonds · nucleic-nucleic
A–B · 607 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Compared structures

4P97 · 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 4P97 · PDBe 4P97

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