MolNFT v1 · #116578 · RNA

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-wt ribozyme in MN2+ at high pH

5DI2 · RNA (48-mer): “Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-wt…”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.52). MolNFT v1 #116578 on GenesisL1: 3D…

PDB: 5DI2
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*U)-D(P*C)- R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3…
Ligands: MN
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (48-mer)	rna	48	—	—
B	5'-R(GPGPGPCPGPU)-D(PC)- R(PUPGPGPGPCPAPGPUPAPCPCPCPA)-3'	rna	20	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 7 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	272	0.52	0.76	18	MN
2	256	0.44	0.72	22	empty
3	80	0.28	0.72	12	MN

Interfaces

1 interface between chains.

A–B · 958 Å² buried · 73 hydrogen bonds · nucleic-nucleic

Compared structures

5DI2 · 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 5DI2 · PDBe 5DI2

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