MolNFT v1 · #141656 · protein + RNA

M. smegmatis trans-translation state 70S ribosome

5ZEY · Tmrna: “M. smegmatis trans-translation state 70S ribosome”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #141656 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZEY
Type: protein + RNA
Length: 607 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tmrna; A-trnafmet; Ssra-binding protein
UniProt: A0QU63
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 3 distinct chains · 17% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tmrna	rna	369	—	—
B	A-trnafmet	rna	77	—	—
C	Ssra-binding protein	protein	161	17% helix, 16% strand	A0QU63

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	303	0.79	0.90	42	empty
2	959	0.74	0.79	50	empty
3	635	0.65	0.76	32	empty
4	278	0.61	0.80	36	empty
5	557	0.61	0.75	26	empty

Interfaces

2 interfaces between chains.

A–C · 1718 Å² buried · 19 hydrogen bonds · protein-nucleic
A–B · 263 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Compared structures

5ZEY · M. smegmatis Trans-translation state 70S ribosome · the same entry in another collection · chain A against A, TM-score 1.00
A0QU63 · AlphaFold monomer V2.0 prediction for ssra-binding protein (A0QU63) · a predicted model of the same protein · chain C against A, TM-score 0.70

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 A0QU63
Elsewhere: RCSB PDB 5ZEY · PDBe 5ZEY · UniProt A0QU63

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