MolNFT v1 · #123965 · protein + RNA

M48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying EIF2 ternary complex and EIF3 I and G subunits relocated to the intersubunit face

5K0Y · TRNA: “M48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying EIF2 ternary…”. Electron microscopy, 20 pockets (best druggability 0.90). MolNFT v1 #123965 on GenesisL1: 3D structure, binding sites…

PDB: 5K0Y
Type: protein + RNA
Length: 7,919 residues
Chains: 42
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA; 18S ribosomal RNA; MRNA; Eukaryotic translation initiation factor 2 subunit 1…
UniProt: G1T2G4, G1TRM4, G1SGX4, G1TK17, G1U7M4, B7NZS8, G1TPG3, O75821, G1TN62, Q5IH81, G1TFM5, G1T8A2, G1TDB3, G1SVB0, G1TZ76, G1SP51, G1TG89, G1TM82, G1TU13, G1TN72, G1TFE8, G1TIB4, G1SJB4, G1U0Q2, G1TJW1, G1SK22, G1TM55, G1SFR8, G1TS40, G1TPV3
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 42 distinct chains · 26% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	TRNA	rna	75	—	—
A	18S ribosomal RNA	rna	1776	—	—
F	MRNA	rna	30	—	—
P	Eukaryotic translation initiation factor 2 subunit 1	protein	266	35% helix, 20% strand	G1T2G4
G	Ribosomal protein US17	protein	158	3% helix, 30% strand	G1TRM4
H	Ribosomal protein US9	protein	141	34% helix, 19% strand	G1SGX4
I	40S ribosomal protein S4	protein	263	15% helix, 30% strand	G1TK17
J	Ribosomal protein US14	protein	53	30% helix, 9% strand	G1U7M4
K	Ribosomal protein S9 (predicted)	protein	182	46% helix, 4% strand	B7NZS8
L	Ribosomal protein US13	protein	137	39% helix, 6% strand	G1TPG3
M	Eukaryotic translation initiation factor 3 subunit G	protein	38	16% helix, 0% strand	O75821
O	Eukaryotic translation initiation factor 3 subunit G	protein	77	27% helix, 36% strand	O75821
Q	Ribosomal protein US12	protein	142	23% helix, 24% strand	—
R	Ribosomal protein ES19	protein	141	50% helix, 8% strand	G1TN62
S	Eukaryotic initiation factor 2 gamma subunit (EIF2-gamma)	protein	422	14% helix, 37% strand	—
T	Eukaryotic translation initiation factor 3 subunit I	protein	329	4% helix, 53% strand	Q5IH81
U	Ribosomal protein US7	protein	191	49% helix, 5% strand	G1TFM5
V	Ribosomal protein ES30	protein	59	20% helix, 0% strand	G1T8A2
W	Ribosomal protein ES25	protein	75	32% helix, 11% strand	G1TDB3
X	Ribosomal protein ES7	protein	190	31% helix, 18% strand	G1SVB0
Y	40S ribosomal protein S27	protein	84	0% helix, 13% strand	G1TZ76
Z	Ribosomal protein US15	protein	150	55% helix, 0% strand	G1SP51
a	Ribosomal protein US8	protein	129	33% helix, 26% strand	G1TG89
b	40S ribosomal protein S21	protein	82	21% helix, 15% strand	G1TM82
c	Ribosomal protein US5	protein	226	29% helix, 22% strand	—
d	Eukaryotic initiation factor 2 subunit beta (EIF2-beta)	protein	17	59% helix, 0% strand	—
e	Ribosomal protein ES17	protein	126	45% helix, 2% strand	G1TU13
f	Ribosomal protein US2	protein	208	34% helix, 13% strand	—
g	Ribosomal protein US3	protein	227	33% helix, 31% strand	—
h	Ribosomal protein US10	protein	104	25% helix, 39% strand	—
i	Ribosomal protein ES1	protein	215	27% helix, 32% strand	G1TN72
j	Ribosomal protein US11	protein	136	19% helix, 20% strand	—
k	Ribosomal protein ES26	protein	99	17% helix, 20% strand	G1TFE8
l	Ribosomal protein ES28	protein	64	0% helix, 45% strand	G1TIB4
m	Ribosomal protein RACK1	protein	313	0% helix, 52% strand	G1SJB4
n	Ribosomal protein US19	protein	127	28% helix, 13% strand	G1U0Q2
o	40S ribosomal protein S8	protein	206	28% helix, 22% strand	G1TJW1
p	Ribosomal protein ES31	protein	71	0% helix, 14% strand	G1SK22
q	40S ribosomal protein S6	protein	237	32% helix, 24% strand	G1TM55
r	40S ribosomal protein S12	protein	124	43% helix, 11% strand	G1SFR8
s	40S ribosomal protein S24	protein	131	36% helix, 24% strand	G1TS40
t	Ribosomal protein ES10	protein	98	34% helix, 16% strand	G1TPV3

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	986	0.90	0.93	124	empty
2	1019	0.87	0.89	101	empty
3	1186	0.87	0.89	89	empty
4	1087	0.86	0.88	112	empty
5	970	0.86	0.87	92	empty

Interfaces

121 interfaces between chains.

A–q · 6445 Å² buried · 157 hydrogen bonds · protein-nucleic
A–I · 4649 Å² buried · 84 hydrogen bonds · protein-nucleic
A–o · 4440 Å² buried · 104 hydrogen bonds · protein-nucleic
A–K · 3978 Å² buried · 91 hydrogen bonds · protein-nucleic
A–Q · 3815 Å² buried · 98 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5K0Y · m48S late-stage initiation complex, purified from rabbit reticulocytes lysates… · the same entry in another collection · chain M against M, 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 G1T2G4
Every structure of UniProt G1TRM4
Every structure of UniProt G1SGX4
Every structure of UniProt G1TK17
Every structure of UniProt G1U7M4
Every structure of UniProt B7NZS8
Every structure of UniProt G1TPG3
Every structure of UniProt O75821
Every structure of UniProt G1TN62
Every structure of UniProt Q5IH81
Every structure of UniProt G1TFM5
Every structure of UniProt G1T8A2
Every structure of UniProt G1TDB3
Every structure of UniProt G1SVB0
Every structure of UniProt G1TZ76
Every structure of UniProt G1SP51
Every structure of UniProt G1TG89
Every structure of UniProt G1TM82
Every structure of UniProt G1TU13
Every structure of UniProt G1TN72
Every structure of UniProt G1TFE8
Every structure of UniProt G1TIB4
Every structure of UniProt G1SJB4
Every structure of UniProt G1U0Q2
Every structure of UniProt G1TJW1
Every structure of UniProt G1SK22
Every structure of UniProt G1TM55
Every structure of UniProt G1SFR8
Every structure of UniProt G1TS40
Every structure of UniProt G1TPV3
Elsewhere: RCSB PDB 5K0Y · PDBe 5K0Y · UniProt G1T2G4 · UniProt G1TRM4 · UniProt G1SGX4 · UniProt G1TK17 · UniProt G1U7M4 · UniProt B7NZS8 · UniProt G1TPG3 · UniProt O75821 · UniProt G1TN62 · UniProt Q5IH81 · UniProt G1TFM5 · UniProt G1T8A2 · UniProt G1TDB3 · UniProt G1SVB0 · UniProt G1TZ76 · UniProt G1SP51 · UniProt G1TG89 · UniProt G1TM82 · UniProt G1TU13 · UniProt G1TN72 · UniProt G1TFE8 · UniProt G1TIB4 · UniProt G1SJB4 · UniProt G1U0Q2 · UniProt G1TJW1 · UniProt G1SK22 · UniProt G1TM55 · UniProt G1SFR8 · UniProt G1TS40 · UniProt G1TPV3

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