Research workbench

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in MN2+

Analyse Two divalent metal ions and conformational changes play roles in the hammerhead… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DH7
Type: RNA
Length: 68 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (48-mer); 5'-R(*GP*GP*GP*CP*GP*UP*DC*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP *CP*A)-3'
Ligands: MN
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (48-mer)	rna	48	—	—
B	5'-R(GPGPGPCPGPUPDCUPGPGPGPCPAPGPUPAPCPCP CPA)-3'	rna	20	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 11 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	311	0.53	0.75	19	MN
2	219	0.42	0.72	22	MN
3	84	0.29	0.73	12	MN

Interfaces

1 interface between chains.

A–B · 956 Å² buried · 80 hydrogen bonds · nucleic-nucleic

Compared structures

5DH7 · Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme… · 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 5DH7 · PDBe 5DH7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.