Research workbench

Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit

Analyse Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FAI
Type: protein + RNA
Length: 7,719 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 40S ribosomal protein S27-a; 40S ribosomal protein S28-a; 40S ribosomal protein S29-a…
EC: 2.7.11.1
UniProt: P35997, Q3E7X9, P41057, P0CX33, P38011, Q99216, P38333, P34078, Q07381, P40160, P32905, P33442, P25443, P05750, P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, P0CX47, P48589, P05756, P06367, Q01855, P0CX51, P02407, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792
Ligands: MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 36 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	40S ribosomal protein S27-a	protein	81	5% helix, 28% strand	P35997
c	40S ribosomal protein S28-a	protein	63	0% helix, 43% strand	Q3E7X9
d	40S ribosomal protein S29-a	protein	37	35% helix, 19% strand	P41057
e	40S ribosomal protein S30-a	protein	48	29% helix, 8% strand	P0CX33
g	Guanine nucleotide-binding protein subunit beta-like protein	protein	317	0% helix, 56% strand	P38011
h	Pre-rRNA-processing protein PNO1	protein	181	56% helix, 19% strand	Q99216
i	Essential nuclear protein 1	protein	262	63% helix, 0% strand	P38333
j	Protein LTV1	protein	46	54% helix, 0% strand	P34078
k	Ribosome biogenesis protein TSR1	protein	670	24% helix, 30% strand	Q07381
l	SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1)	protein	286	42% helix, 21% strand	P40160
2	20S ribosomal RNA	rna	1775	—	—
A	40S ribosomal protein S0-a	protein	206	34% helix, 15% strand	P32905
B	40S ribosomal protein S1-a	protein	214	33% helix, 35% strand	P33442
C	40S ribosomal protein S2	protein	217	26% helix, 26% strand	P25443
D	40S ribosomal protein S3	protein	202	37% helix, 30% strand	P05750
E	40S ribosomal protein S4-a	protein	260	13% helix, 33% strand	P0CX35
F	40S ribosomal protein S5	protein	206	49% helix, 4% strand	P26783
G	40S ribosomal protein S6-a	protein	232	28% helix, 27% strand	P0CX37
H	40S ribosomal protein S7-a	protein	184	35% helix, 22% strand	P26786
I	40S ribosomal protein S8-a	protein	188	27% helix, 22% strand	P0CX39
J	40S ribosomal protein S9-a	protein	185	53% helix, 4% strand	O13516
L	40S ribosomal protein S11-a	protein	140	3% helix, 34% strand	P0CX47
M	40S ribosomal protein S12	protein	125	38% helix, 19% strand	P48589
N	40S ribosomal protein S13	protein	150	56% helix, 1% strand	P05756
O	40S ribosomal protein S14-a	protein	127	29% helix, 28% strand	P06367
P	40S ribosomal protein S15	protein	127	32% helix, 13% strand	Q01855
Q	40S ribosomal protein S16-a	protein	127	35% helix, 21% strand	P0CX51
R	40S ribosomal protein S17-a	protein	125	55% helix, 5% strand	P02407
S	40S ribosomal protein S18-a	protein	135	44% helix, 7% strand	P0CX55
T	40S ribosomal protein S19-a	protein	143	48% helix, 16% strand	P07280
U	40S ribosomal protein S20	protein	103	26% helix, 48% strand	P38701
V	40S ribosomal protein S21-a	protein	87	18% helix, 26% strand	P0C0V8
W	40S ribosomal protein S22-a	protein	129	32% helix, 25% strand	P0C0W1
X	40S ribosomal protein S23-a	protein	144	21% helix, 28% strand	P0CX29
Y	40S ribosomal protein S24-a	protein	134	39% helix, 26% strand	P0CX31
Z	40S ribosomal protein S25-a	protein	63	54% helix, 6% strand	Q3E792

Ligands and binding sites

MG · Magnesium ion · metal · 46 copies · chains 2, N, C, L, E
ZN · Zinc ion · metal · 2 copies · chains b, d

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	877	0.88	0.91	88	empty
2	871	0.88	0.91	76	MG
3	896	0.86	0.89	90	empty
4	1000	0.86	0.88	76	empty
5	1196	0.86	0.88	121	empty

Interfaces

99 interfaces between chains.

2–G · 5365 Å² buried · 119 hydrogen bonds · protein-nucleic
2–E · 3919 Å² buried · 67 hydrogen bonds · protein-nucleic
2–I · 3815 Å² buried · 113 hydrogen bonds · protein-nucleic
2–J · 3599 Å² buried · 63 hydrogen bonds · protein-nucleic
2–X · 3513 Å² buried · 64 hydrogen bonds · protein-nucleic

Compared structures

6FAI · Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit · the same entry in another collection · chain 2 against 2, 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
Every structure of UniProt P35997
Every structure of UniProt Q3E7X9
Every structure of UniProt P41057
Every structure of UniProt P0CX33
Every structure of UniProt P38011
Every structure of UniProt Q99216
Every structure of UniProt P38333
Every structure of UniProt P34078
Every structure of UniProt Q07381
Every structure of UniProt P40160
Every structure of UniProt P32905
Every structure of UniProt P33442
Every structure of UniProt P25443
Every structure of UniProt P05750
Every structure of UniProt P0CX35
Every structure of UniProt P26783
Every structure of UniProt P0CX37
Every structure of UniProt P26786
Every structure of UniProt P0CX39
Every structure of UniProt O13516
Every structure of UniProt P0CX47
Every structure of UniProt P48589
Every structure of UniProt P05756
Every structure of UniProt P06367
Every structure of UniProt Q01855
Every structure of UniProt P0CX51
Every structure of UniProt P02407
Every structure of UniProt P0CX55
Every structure of UniProt P07280
Every structure of UniProt P38701
Every structure of UniProt P0C0V8
Every structure of UniProt P0C0W1
Every structure of UniProt P0CX29
Every structure of UniProt P0CX31
Every structure of UniProt Q3E792
Elsewhere: RCSB PDB 6FAI · PDBe 6FAI · UniProt P35997 · UniProt Q3E7X9 · UniProt P41057 · UniProt P0CX33 · UniProt P38011 · UniProt Q99216 · UniProt P38333 · UniProt P34078 · UniProt Q07381 · UniProt P40160 · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P05750 · UniProt P0CX35 · UniProt P26783 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P48589 · UniProt P05756 · UniProt P06367 · UniProt Q01855 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt P38701 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt Q3E792

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