MolNFT v1 · #105816 · RNA

Crystal structure of the in-line aligned ENV22 twister ribozyme soaked with MN2+

4RGF: “Crystal structure of the in-line aligned ENV22 twister ribozyme soaked with MN2+”. X-ray diffraction, 3 ligands (K, MN, MG), 9 pockets (best druggability 0.70). MolNFT v1 #105816 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4RGF
Type: RNA
Length: 167 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ENV22 twister ribozyme
Ligands: K, MN, MG
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ENV22 twister ribozyme	rna	56	—	—
C	ENV22 twister ribozyme	rna	55	—	—

Ligands and binding sites

K · Potassium ion · metal · 14 copies · chains A, B, C
MN · Manganese (II) ion · metal · 11 copies · chains A, B, C
MG · Magnesium ion · metal · chains C

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

Pockets

9 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	653	0.70	0.79	46	MG, MN, K
2	300	0.65	0.82	25	K
3	148	0.57	0.83	17	K
4	308	0.56	0.77	26	MN, K
5	162	0.51	0.80	15	MN

Interfaces

1 interface between chains.

B–C · 303 Å² buried · 9 hydrogen bonds · nucleic-nucleic

Compared structures

4RGF · Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+ · 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 4RGF · PDBe 4RGF

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