MolNFT v1 · #107586 · protein + RNA

40S-EIF1-EIF1A-EIF3-EIF3J translation initiation complex from lachancea kluyveri

4UER: “40S-EIF1-EIF1A-EIF3-EIF3J translation initiation complex from lachancea kluyveri”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.89). MolNFT v1 #107586 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4UER
Type: protein + RNA
Length: 8,377 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EIF1A; ES28; ES8; ES7; ES1; ES26; ES27; ES10; ES25; ES31; 18S rRNA; US2; US3; US4; US5…
Ligands: ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 39 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	EIF1A	protein	100	15% helix, 36% strand	—
1	ES28	protein	63	0% helix, 46% strand	—
2	ES8	protein	188	28% helix, 24% strand	—
3	ES7	protein	184	35% helix, 21% strand	—
4	ES1	protein	214	28% helix, 25% strand	—
5	ES26	protein	97	14% helix, 19% strand	—
6	ES27	protein	81	6% helix, 22% strand	—
7	ES10	protein	96	39% helix, 11% strand	—
8	ES25	protein	70	34% helix, 11% strand	—
9	ES31	protein	71	0% helix, 20% strand	—
A	18S rRNA	rna	1781	—	—
B	US2	protein	206	32% helix, 16% strand	—
C	US3	protein	223	36% helix, 26% strand	—
D	US4	protein	185	53% helix, 2% strand	—
E	US5	protein	217	31% helix, 28% strand	—
F	EIF1	protein	83	30% helix, 40% strand	—
G	US7	protein	206	48% helix, 5% strand	—
H	US8	protein	129	32% helix, 26% strand	—
I	US9	protein	141	33% helix, 19% strand	—
J	US10	protein	107	24% helix, 40% strand	—
K	US11	protein	127	23% helix, 19% strand	—
L	US12	protein	144	23% helix, 24% strand	—
M	US13	protein	145	34% helix, 3% strand	—
N	US14	protein	53	32% helix, 9% strand	—
O	US15	protein	150	56% helix, 0% strand	—
P	ES24	protein	134	38% helix, 26% strand	—
Q	US17	protein	155	7% helix, 35% strand	—
R	RACK1	protein	318	0% helix, 56% strand	—
S	US19	protein	124	35% helix, 14% strand	—
T	ES19	protein	143	46% helix, 10% strand	—
U	ES12	protein	124	40% helix, 6% strand	—
V	ES17	protein	120	50% helix, 5% strand	—
W	ES4	protein	260	15% helix, 27% strand	—
X	ES30	protein	60	30% helix, 2% strand	—
Y	ES6	protein	226	31% helix, 27% strand	—
Z	ES21	protein	87	17% helix, 14% strand	—
a	EIF3A	protein	449	72% helix, 2% strand	—
b	EIF3B	protein	572	3% helix, 38% strand	—
c	EIF3C	protein	544	68% helix, 2% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains 5, 6, 9, N

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	1146	0.89	0.91	114	empty
2	1184	0.89	0.91	93	empty
3	822	0.86	0.89	78	empty
4	954	0.86	0.88	83	empty
5	1058	0.85	0.87	88	empty

Interfaces

104 interfaces between chains.

A–Y · 4989 Å² buried · 127 hydrogen bonds · protein-nucleic
A–W · 4050 Å² buried · 77 hydrogen bonds · protein-nucleic
2–A · 3987 Å² buried · 126 hydrogen bonds · protein-nucleic
A–L · 3632 Å² buried · 82 hydrogen bonds · protein-nucleic
A–D · 3587 Å² buried · 62 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

4UER · 40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri · the same entry in another collection · chain 8 against 8, 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 4UER · PDBe 4UER

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