MolNFT v1 · #57091 · RNA

Capturing the structure of a catalytic RNA intermediate: RNA hammerhead ribozyme, MN(II)-soaked

300D: “Capturing the structure of a catalytic RNA intermediate: RNA hammerhead ribozyme, MN(II)-soaked”. X-ray diffraction, 1 ligand (MN), 1 pocket (best druggability 0.28). MolNFT v1 #57091 on GenesisL1: 3D structure, binding sites and…

PDB: 300D
Type: RNA
Length: 41 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA hammerhead ribozyme
Ligands: MN
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA hammerhead ribozyme	rna	16	—	—
B	RNA hammerhead ribozyme	rna	25	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.28	0.73	10	empty

Interfaces

1 interface between chains.

A–B · 1055 Å² buried · 111 hydrogen bonds · nucleic-nucleic

Compared structures

300D · Capturing the structure of a catalytic RNA intermediate: RNA 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 300D · PDBe 300D

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