MolNFT v1 · #125843 · protein + RNA

Structure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation initiation

5LL6 · 18S ribosomal RNA: “Structure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation initiation”. Electron microscopy, 3 ligands (SF4, ANP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #125843 on…

PDB: 5LL6
Type: protein + RNA
Length: 4,754 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S ribosomal RNA; 40S ribosomal protein S0-a; 40S ribosomal protein S1-a; 40S ribosomal…
UniProt: P32905, P33442, P25443, P0CX35, P0CX37, P26786, P0CX39, O13516, P0CX47, P05756, P06367, P0C0V8, P0C0W1, P0CX29, P0CX31, P39938, P35997, P0CX33, Q03195
Ligands: SF4, ANP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 20 distinct chains · 28% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S ribosomal RNA	rna	1325	—	—
P	40S ribosomal protein S0-a	protein	206	31% helix, 11% strand	P32905
Q	40S ribosomal protein S1-a	protein	214	27% helix, 21% strand	P33442
R	40S ribosomal protein S2	protein	226	29% helix, 25% strand	P25443
S	40S ribosomal protein S4-a	protein	260	15% helix, 26% strand	P0CX35
T	40S ribosomal protein S6-a	protein	226	25% helix, 21% strand	P0CX37
U	40S ribosomal protein S7-a	protein	184	30% helix, 17% strand	P26786
V	40S ribosomal protein S8-a	protein	188	25% helix, 27% strand	P0CX39
W	40S ribosomal protein S9-a	protein	185	50% helix, 2% strand	O13516
X	40S ribosomal protein S11-a	protein	155	3% helix, 30% strand	P0CX47
Y	40S ribosomal protein S13	protein	150	54% helix, 0% strand	P05756
Z	40S ribosomal protein S14-a	protein	127	28% helix, 14% strand	P06367
a	40S ribosomal protein S21-a	protein	87	21% helix, 21% strand	P0C0V8
b	40S ribosomal protein S22-a	protein	129	34% helix, 21% strand	P0C0W1
c	40S ribosomal protein S23-a	protein	144	19% helix, 18% strand	P0CX29
d	40S ribosomal protein S24-a	protein	132	37% helix, 24% strand	P0CX31
e	40S ribosomal protein S26-a	protein	97	11% helix, 20% strand	P39938
f	40S ribosomal protein S27-a	protein	81	7% helix, 20% strand	P35997
g	40S ribosomal protein S30-a	protein	60	27% helix, 0% strand	P0CX33
h	Translation initiation factor RLI1	protein	578	31% helix, 16% strand	Q03195

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains h
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains h
MG · Magnesium ion · metal · chains h

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	776	0.87	0.91	92	empty
2	782	0.87	0.91	64	empty
3	667	0.86	0.91	68	empty
4	724	0.86	0.89	69	empty
5	595	0.85	0.91	63	empty

Interfaces

53 interfaces between chains.

2–T · 5340 Å² buried · 110 hydrogen bonds · protein-nucleic
2–S · 4218 Å² buried · 64 hydrogen bonds · protein-nucleic
2–V · 4006 Å² buried · 99 hydrogen bonds · protein-nucleic
2–c · 3968 Å² buried · 77 hydrogen bonds · protein-nucleic
2–W · 3758 Å² buried · 69 hydrogen bonds · protein-nucleic

Compared structures

5LL6 · Structure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation… · the same entry in another collection · chain h against h, 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 P32905
Every structure of UniProt P33442
Every structure of UniProt P25443
Every structure of UniProt P0CX35
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 P05756
Every structure of UniProt P06367
Every structure of UniProt P0C0V8
Every structure of UniProt P0C0W1
Every structure of UniProt P0CX29
Every structure of UniProt P0CX31
Every structure of UniProt P39938
Every structure of UniProt P35997
Every structure of UniProt P0CX33
Every structure of UniProt Q03195
Elsewhere: RCSB PDB 5LL6 · PDBe 5LL6 · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P0CX35 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P05756 · UniProt P06367 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt P39938 · UniProt P35997 · UniProt P0CX33 · UniProt Q03195

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