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Structure of ribosome-bound cricket paralysis virus ires RNA

Analyse Structure of ribosome-bound cricket paralysis virus ires RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NOQ
Type: protein + RNA
Length: 845 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Crpv ires; 18S ribosomal RNA; 25S ribosomal RNA; 40S ribosomal protein S5; 60S ribosomal…
UniProt: P26783, P53030, Q3E757
Pockets: 20 · best druggability 0.70

Structure

electron microscopy · 8 distinct chains · 32% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Crpv ires	rna	190	—	—
B	18S ribosomal RNA	rna	46	—	—
C	18S ribosomal RNA	rna	13	—	—
D	18S ribosomal RNA	rna	15	—	—
E	25S ribosomal RNA	rna	53	—	—
F	40S ribosomal protein S5	protein	150	54% helix, 9% strand	P26783
G	60S ribosomal protein L1	protein	213	39% helix, 25% strand	P53030
H	60S ribosomal protein L11-B	protein	165	2% helix, 5% strand	Q3E757

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	52	0.70	0.97	22	empty
2	723	0.69	0.77	71	empty
3	113	0.65	0.88	30	empty
4	85	0.64	0.90	18	empty
5	320	0.62	0.80	26	empty

Interfaces

9 interfaces between chains.

E–G · 1338 Å² buried · 72 hydrogen bonds · protein-nucleic
C–D · 914 Å² buried · 66 hydrogen bonds · nucleic-nucleic
A–B · 598 Å² buried · 106 hydrogen bonds · nucleic-nucleic
A–G · 542 Å² buried · 63 hydrogen bonds · protein-nucleic
A–F · 372 Å² buried · 19 hydrogen bonds · protein-nucleic

Compared structures

2NOQ · Structure of ribosome-bound cricket paralysis virus IRES RNA · the same entry in another collection · chain H against H, TM-score 1.00
Q3E757 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L11-B (Q3E757) · a predicted model of the same protein · chain H against A, TM-score 0.76

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 P26783
Every structure of UniProt P53030
Every structure of UniProt Q3E757
Elsewhere: RCSB PDB 2NOQ · PDBe 2NOQ · UniProt P26783 · UniProt P53030 · UniProt Q3E757

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