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Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing

Analyse Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7YCH
Type: RNA
Length: 404 nucleotides
Chains: 2
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.09
Source: Tetrahymena; SYNTHETIC CONSTRUCT
Molecule: RNA (5'-R(*CP*CP*CP*UP*CP*UP*AP*AP*AP*CP*C)-3'); RNA (393-mer)
Ligands: GTP, MG
Pockets: 17 · best druggability 0.74

Structure

electron microscopy · resolution 3.09 · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	RNA (5'-R(CPCPCPUPCPUPAPAPAPCP*C)-3')	rna	11	—	—
N	RNA (393-mer)	rna	393	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains B, N
MG · Magnesium ion · metal · 3 copies · chains B, N

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.74	0.93	20	empty
2	1100	0.73	0.77	64	empty
3	965	0.69	0.75	44	empty
4	919	0.67	0.75	54	empty
5	373	0.66	0.81	30	empty

Interfaces

1 interface between chains.

B–N · 812 Å² buried · 62 hydrogen bonds · nucleic-nucleic

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7YCH · PDBe 7YCH

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