MolNFT v1 · #67919 · protein + RNA

Tmrna-smpb: a journey to the center of the bacterial ribosome

3IYQ: “Tmrna-smpb: a journey to the center of the bacterial ribosome”. Electron microscopy, 17 pockets (best druggability 0.74). MolNFT v1 #67919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IYQ
Type: protein + RNA
Length: 471 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tmrna; Ssra-binding protein
UniProt: Q8RR57
Pockets: 17 · best druggability 0.74

Structure

electron microscopy · 2 distinct chains · 16% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tmrna	rna	349	—	—
B	Ssra-binding protein	protein	122	16% helix, 25% strand	Q8RR57

Pockets

17 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	832	0.74	0.79	41	empty
2	278	0.63	0.82	19	empty
3	202	0.53	0.79	14	empty
4	196	0.51	0.78	15	empty
5	126	0.46	0.79	13	empty

Interfaces

1 interface between chains.

A–B · 1986 Å² buried · 77 hydrogen bonds · protein-nucleic

Compared structures

3IYQ · tmRNA-SmpB: a journey to the center of the bacterial ribosome · the same entry in another collection · chain A against A, TM-score 1.00
Q8RR57 · AlphaFold monomer V2.0 prediction for ssra-binding protein (Q8RR57) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 Q8RR57
Elsewhere: RCSB PDB 3IYQ · PDBe 3IYQ · UniProt Q8RR57

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