MolNFT v2 · #15674 · RNA

Crystal structure of the specificity domain of Ribonuclease P RNA

1NBS: “Crystal structure of the specificity domain of Ribonuclease P RNA”. X-ray diffraction at 3.15, 2 ligands (PB, MG), 10 pockets (best druggability 0.72). MolNFT v2 #15674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NBS
Type: RNA
Length: 270 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.15
Source: Bacillus subtilis
Molecule: Ribonuclease P RNA
Ligands: PB, MG
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · resolution 3.15 · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease P RNA	rna	120	—	—
B	Ribonuclease P RNA	rna	150	—	—

Ligands and binding sites

PB · Lead (II) ion · metal · 23 copies · chains A, B
MG · Magnesium ion · metal · 12 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	854	0.72	0.78	55	PB, MG
2	541	0.71	0.81	43	MG, PB
3	544	0.60	0.75	26	MG
4	259	0.56	0.79	27	MG
5	284	0.48	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 583 Å² buried · 28 hydrogen bonds · nucleic-nucleic

Compared structures

1NBS · Crystal structure of the specificity domain of ribonuclease P RNA · 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 1NBS · PDBe 1NBS

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