MolNFT v1 · #176492 · protein + RNA

Mycoplasma genitalium RNase R in complex with double-stranded RNA

7DOL · Ribonuclease R: “Mycoplasma genitalium RNase R in complex with double-stranded RNA”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.82). MolNFT v1 #176492 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7DOL
Type: protein + RNA
Length: 571 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease R; RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
EC: 3.1.13.1
UniProt: P47350
Ligands: MG
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease R (EC 3.1.13.1)	protein	565	35% helix, 26% strand	P47350
C	RNA (5'-R(PAPAPAPAPAPA)-3')	rna	6	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1041	0.82	0.83	70	empty
2	188	0.62	0.83	29	empty
3	122	0.58	0.85	17	empty
4	86	0.47	0.81	18	empty
5	123	0.44	0.77	15	empty

Interfaces

1 interface between chains.

A–C · 1042 Å² buried · 31 hydrogen bonds · protein-nucleic

Compared structures

7DOL · Mycoplasma genitalium RNase R in complex with double-stranded RNA · the same entry in another collection · chain A against A, TM-score 1.00
P47350 · AlphaFold monomer V2.0 prediction for ribonuclease R (P47350) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P47350
Elsewhere: RCSB PDB 7DOL · PDBe 7DOL · UniProt P47350

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