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Core of mammalian 80S pre-ribosome in complex with trnas fitted to a 10.6A cryo-EM MAP: rotated pre state 2

Analyse Core of mammalian 80S pre-ribosome in complex with trnas fitted to a 10.6A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J0Q
Type: protein + RNA
Length: 1,520 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 40S ribosomal RNA fragment; Ribosomal protein S15; Ribosomal protein S23; Ribosomal…
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 20 distinct chains · 22% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	40S ribosomal RNA fragment	rna	48	—	—
c	40S ribosomal RNA fragment	rna	17	—	—
d	40S ribosomal RNA fragment	rna	7	—	—
g	40S ribosomal RNA fragment	rna	31	—	—
G	40S ribosomal RNA fragment	rna	13	—	—
f	40S ribosomal RNA fragment	rna	21	—	—
h	40S ribosomal RNA fragment	rna	111	—	—
S	Ribosomal protein S15	protein	125	39% helix, 12% strand	—
L	Ribosomal protein S23	protein	141	23% helix, 28% strand	—
X	Ribosomal protein S30	protein	68	34% helix, 0% strand	—
2	60S ribosomal RNA fragment	rna	112	—	—
3	60S ribosomal RNA fragment	rna	12	—	—
9	60S ribosomal RNA fragment	rna	19	—	—
7	60S ribosomal RNA fragment	rna	50	—	—
B	Ribosomal protein L10A	protein	213	14% helix, 0% strand	—
J	Ribosomal protein L10	protein	208	24% helix, 12% strand	—
k	Ribosomal protein L11	protein	165	13% helix, 4% strand	—
Y, W	TRNA	rna	77	—	—
y	MRNA fragment	rna	3	—	—
w	MRNA fragment	rna	2	—	—

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	975	0.76	0.79	133	empty
2	740	0.75	0.81	110	empty
3	1019	0.75	0.78	99	empty
4	933	0.73	0.78	66	empty
5	432	0.68	0.81	43	empty

Interfaces

41 interfaces between chains.

9–k · 1209 Å² buried · 156 hydrogen bonds · protein-nucleic
a–X · 1173 Å² buried · 24 hydrogen bonds · protein-nucleic
g–G · 779 Å² buried · 58 hydrogen bonds · nucleic-nucleic
a–L · 676 Å² buried · 15 hydrogen bonds · protein-nucleic
3–B · 638 Å² buried · 96 hydrogen bonds · protein-nucleic

Compared structures

3J0Q · Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map… · the same entry in another collection · chain a against a, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3J0Q · PDBe 3J0Q

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