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The structural basis of hammerhead ribozyme self-cleavage

Analyse The structural basis of hammerhead ribozyme self-cleavage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 379D
Type: RNA
Length: 41 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'); RNA (5'…
Ligands: CO
Pockets: 2 · best druggability 0.26

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'- R(GPUPGPGPUPCPUPGPAPUPGPAPGPGPCPC)-3')	rna	16	—	—
B	RNA (5'- R(GPGPCPCPGPAPAPAPCPUPCPGPUPAPAPGPA PGPUPCPAPCPCPAP*C)-3')	rna	25	—	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 8 copies · chains A, B

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	67	0.26	0.73	11	empty
2	81	0.26	0.71	13	CO

Interfaces

1 interface between chains.

A–B · 1030 Å² buried · 69 hydrogen bonds · nucleic-nucleic

Compared structures

379D · The structural basis of hammerhead ribozyme self-cleavage · 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 379D · PDBe 379D

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