MolNFT v1 · #28178 · protein + RNA

Rrf domain I in complex with the 50S ribosomal subunit from deinococcus radiodurans

1Y69 · 23S ribosomal RNA: “Rrf domain I in complex with the 50S ribosomal subunit from deinococcus radiodurans”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #28178 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1Y69
Type: protein + RNA
Length: 3,217 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L16; 50S ribosomal protein…
UniProt: Q9RXJ5, Q9RY65, P0A805
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	23S ribosomal RNA	rna	2766	—	—
9	5S ribosomal RNA	rna	118	—	—
K	50S ribosomal protein L16	protein	136	12% helix, 11% strand	Q9RXJ5
U	50S ribosomal protein L27	protein	84	0% helix, 33% strand	Q9RY65
8	Ribosome-recycling factor	protein	113	74% helix, 0% strand	P0A805

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.88	0.90	109	empty
2	590	0.84	0.90	60	empty
3	504	0.84	0.91	58	empty
4	560	0.83	0.90	62	empty
5	330	0.79	0.90	39	empty

Interfaces

9 interfaces between chains.

0–K · 2760 Å² buried · 51 hydrogen bonds · protein-nucleic
0–U · 2390 Å² buried · 47 hydrogen bonds · protein-nucleic
0–8 · 1051 Å² buried · 35 hydrogen bonds · protein-nucleic
0–9 · 843 Å² buried · 24 hydrogen bonds · nucleic-nucleic
9–K · 268 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

1Y69 · RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans · the same entry in another collection · chain 8 against 8, TM-score 1.00
P0A805 · AlphaFold monomer V2.0 prediction for ribosome-recycling factor (P0A805) · a predicted model of the same protein · chain 8 against A, TM-score 0.89
Q9RXJ5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (Q9RXJ5) · a predicted model of the same protein · chain K against A, TM-score 0.89
Q9RY65 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L27 (Q9RY65) · a predicted model of the same protein · chain U against A, TM-score 0.82

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 Q9RXJ5
Every structure of UniProt Q9RY65
Every structure of UniProt P0A805
Elsewhere: RCSB PDB 1Y69 · PDBe 1Y69 · UniProt Q9RXJ5 · UniProt Q9RY65 · UniProt P0A805

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