MolNFT v1 · #149589 · protein + RNA

Cryo-EM structure of a late human pre-40S ribosomal subunit - state a

6G4W · 18S ribosomal RNA: “Cryo-EM structure of a late human pre-40S ribosomal subunit - state a”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #149589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6G4W
Type: protein + RNA
Length: 6,920 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S ribosomal RNA; 40S ribosomal protein S17; 40S ribosomal protein S27; 40S ribosomal…
EC: 2.1.1.-
UniProt: P08708, P42677, P61247, P62857, P62701, P62861, P46782, P62081, P62753, P62851, P62847, Q9NRX1, P62266, Q13895, P62244, Q2NL82, P39019, P62269, P62249, P62841, P62263, P62277, P62280, P46781, P62241, Q9UI30, O43709
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 31 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S ribosomal RNA	rna	1563	—	—
R	40S ribosomal protein S17	protein	81	59% helix, 0% strand	P08708
b	40S ribosomal protein S27	protein	82	7% helix, 27% strand	P42677
B	40S ribosomal protein S3A	protein	213	28% helix, 31% strand	P61247
c	40S ribosomal protein S28	protein	61	0% helix, 41% strand	P62857
E	40S ribosomal protein S4, X isoform	protein	262	13% helix, 27% strand	P62701
e	40S ribosomal protein S30	protein	55	20% helix, 0% strand	P62861
F	40S ribosomal protein S5	protein	189	43% helix, 7% strand	P46782
H	40S ribosomal protein S7	protein	186	37% helix, 22% strand	P62081
G	40S ribosomal protein S6	protein	230	27% helix, 24% strand	P62753
Z	40S ribosomal protein S25	protein	72	43% helix, 14% strand	P62851
Y	40S ribosomal protein S24	protein	124	28% helix, 29% strand	P62847
x	RNA-binding protein PNO1	protein	175	50% helix, 19% strand	Q9NRX1
X	40S ribosomal protein S23	protein	141	22% helix, 26% strand	P62266
w	Bystin	protein	248	67% helix, 0% strand	Q13895
W	40S ribosomal protein S15A	protein	129	29% helix, 27% strand	P62244
u	Pre-rRNA-processing protein TSR1 homolog	protein	628	21% helix, 26% strand	Q2NL82
t	Unknown	protein	18	0% helix, 6% strand	—
T	40S ribosomal protein S19	protein	144	52% helix, 9% strand	P39019
S	40S ribosomal protein S18	protein	143	37% helix, 6% strand	P62269
Q	40S ribosomal protein S16	protein	139	37% helix, 19% strand	P62249
P	40S ribosomal protein S15	protein	120	35% helix, 16% strand	P62841
O	40S ribosomal protein S14	protein	135	21% helix, 26% strand	P62263
N	40S ribosomal protein S13	protein	149	50% helix, 0% strand	P62277
L	40S ribosomal protein S11	protein	151	7% helix, 26% strand	P62280
J	40S ribosomal protein S9	protein	180	48% helix, 4% strand	P46781
I	40S ribosomal protein S8	protein	205	29% helix, 27% strand	P62241
s	RRP12	protein	768	86% helix, 0% strand	—
r	Multifunctional methyltransferase subunit TRM112-like protein	protein	118	33% helix, 23% strand	Q9UI30
q	Probable 18S rRNA (guanine-N(7))-methyltransferase (EC 2.1.1.-)	protein	192	41% helix, 24% strand	O43709
k	Unknown helix	protein	19	89% helix, 0% strand	—

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	798	0.84	0.87	108	empty
2	660	0.83	0.88	98	empty
3	1082	0.83	0.84	146	empty
4	1000	0.81	0.82	132	empty
5	959	0.81	0.83	142	empty

Interfaces

62 interfaces between chains.

2–I · 2122 Å² buried · 16 hydrogen bonds · protein-nucleic
2–E · 2004 Å² buried · 32 hydrogen bonds · protein-nucleic
2–G · 1930 Å² buried · 16 hydrogen bonds · protein-nucleic
2–N · 1509 Å² buried · 14 hydrogen bonds · protein-nucleic
2–J · 1391 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

6G4W · Cryo-EM structure of a late human pre-40S ribosomal subunit - State A · the same entry in another collection · chain F against F, 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 P08708
Every structure of UniProt P42677
Every structure of UniProt P61247
Every structure of UniProt P62857
Every structure of UniProt P62701
Every structure of UniProt P62861
Every structure of UniProt P46782
Every structure of UniProt P62081
Every structure of UniProt P62753
Every structure of UniProt P62851
Every structure of UniProt P62847
Every structure of UniProt Q9NRX1
Every structure of UniProt P62266
Every structure of UniProt Q13895
Every structure of UniProt P62244
Every structure of UniProt Q2NL82
Every structure of UniProt P39019
Every structure of UniProt P62269
Every structure of UniProt P62249
Every structure of UniProt P62841
Every structure of UniProt P62263
Every structure of UniProt P62277
Every structure of UniProt P62280
Every structure of UniProt P46781
Every structure of UniProt P62241
Every structure of UniProt Q9UI30
Every structure of UniProt O43709
Elsewhere: RCSB PDB 6G4W · PDBe 6G4W · UniProt P08708 · UniProt P42677 · UniProt P61247 · UniProt P62857 · UniProt P62701 · UniProt P62861 · UniProt P46782 · UniProt P62081 · UniProt P62753 · UniProt P62851 · UniProt P62847 · UniProt Q9NRX1 · UniProt P62266 · UniProt Q13895 · UniProt P62244 · UniProt Q2NL82 · UniProt P39019 · UniProt P62269 · UniProt P62249 · UniProt P62841 · UniProt P62263 · UniProt P62277 · UniProt P62280 · UniProt P46781 · UniProt P62241 · UniProt Q9UI30 · UniProt O43709

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