Research workbench

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

Analyse Tmrna-smpb: a journey to the center of the bacterial ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IYR
Type: protein + RNA
Length: 492 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tmrna; Ssra-binding protein
UniProt: Q8RR57
Pockets: 19 · best druggability 0.58

Structure

electron microscopy · 2 distinct chains · 13% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tmrna	rna	349	—	—
B	Ssra-binding protein	protein	143	13% helix, 24% strand	Q8RR57

Pockets

19 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	320	0.58	0.78	23	empty
2	337	0.56	0.76	22	empty
3	226	0.53	0.78	20	empty
4	264	0.52	0.76	20	empty
5	180	0.49	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 2619 Å² buried · 101 hydrogen bonds · protein-nucleic

Compared structures

3IYR · 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 0.74

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 3IYR · PDBe 3IYR · UniProt Q8RR57

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