Research workbench

SARS-cov-2 NSP1 and rabbit 40S ribosome complex

Analyse SARS-cov-2 NSP1 and rabbit 40S ribosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JQB
Type: protein + RNA
Length: 6,556 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRNA; ES25; 40S ribosomal protein sa; 40S ribosomal protein S26; ES1; US5; ES28…
EC: 4.2.99.18
UniProt: G1TDB3, G1TLT8, G1TFE8, G1SS70, G1TIB4, G1TNM3, G1T8A2, G1TFM5, G1SK22, G1TM55, G1SJB4, G1SVB0, G1TJW1, B7NZS8, G1TPV3, G1SFR8, G1U0Q2, G1SGX4, G1TU13, G1TPG3, G1TN62, G1SIZ2, G1TM82, A0A5F9CBF4, P0DTD1, G1TK17, G1TRM4, G1SP51, G1U472, G1TG89, G1SZ47, G1TZ76
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 34 distinct chains · 27% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RRNA	rna	1697	—	—
a	ES25	protein	75	37% helix, 19% strand	G1TDB3
B	40S ribosomal protein sa	protein	217	39% helix, 14% strand	G1TLT8
b	40S ribosomal protein S26	protein	101	13% helix, 22% strand	G1TFE8
C	ES1	protein	213	27% helix, 32% strand	G1SS70
D	US5	protein	221	30% helix, 27% strand	—
d	ES28	protein	62	0% helix, 45% strand	G1TIB4
E	Ribosomal protein S3 (EC 4.2.99.18)	protein	228	32% helix, 23% strand	G1TNM3
f	ES30	protein	57	30% helix, 0% strand	G1T8A2
G	US7	protein	185	42% helix, 3% strand	G1TFM5
g	ES31	protein	68	0% helix, 21% strand	G1SK22
H	ES6	protein	237	32% helix, 19% strand	G1TM55
h	RACK1	protein	313	0% helix, 38% strand	G1SJB4
I	ES7	protein	185	32% helix, 23% strand	G1SVB0
J	ES8	protein	206	27% helix, 27% strand	G1TJW1
K	US4	protein	185	49% helix, 5% strand	B7NZS8
L	S10_PLECTIN domain-containing protein	protein	96	34% helix, 11% strand	G1TPV3
N	ES12	protein	117	21% helix, 11% strand	G1SFR8
Q	US19	protein	129	23% helix, 12% strand	G1U0Q2
R	Uncharacterized protein	protein	142	34% helix, 14% strand	G1SGX4
S	ES17	protein	132	36% helix, 5% strand	G1TU13
T	US13	protein	144	37% helix, 9% strand	G1TPG3
U	Uncharacterized protein	protein	141	39% helix, 6% strand	G1TN62
V	US10	protein	100	17% helix, 36% strand	G1SIZ2
W	40S ribosomal protein S21	protein	83	20% helix, 24% strand	G1TM82
Z	40S ribosomal protein S24	protein	124	31% helix, 28% strand	A0A5F9CBF4
F	Host translation inhibitor NSP1	protein	36	56% helix, 0% strand	P0DTD1
M	40S ribosomal protein S4	protein	263	16% helix, 27% strand	G1TK17
O	US17	protein	158	3% helix, 28% strand	G1TRM4
P	US15	protein	150	52% helix, 0% strand	G1SP51
X	Uncharacterized protein	protein	136	22% helix, 18% strand	G1U472
Y	US8	protein	129	31% helix, 27% strand	G1TG89
c	Uncharacterized protein	protein	142	21% helix, 24% strand	G1SZ47
e	ES27	protein	84	5% helix, 11% strand	G1TZ76

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	976	0.89	0.91	90	empty
2	748	0.88	0.92	103	empty
3	997	0.88	0.90	77	empty
4	922	0.87	0.89	94	empty
5	1148	0.86	0.88	127	empty

Interfaces

89 interfaces between chains.

A–H · 5442 Å² buried · 134 hydrogen bonds · protein-nucleic
A–J · 4289 Å² buried · 113 hydrogen bonds · protein-nucleic
A–M · 4010 Å² buried · 75 hydrogen bonds · protein-nucleic
A–K · 3648 Å² buried · 75 hydrogen bonds · protein-nucleic
A–c · 3540 Å² buried · 72 hydrogen bonds · protein-nucleic

Compared structures

7JQB · SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex · the same entry in another collection · chain a against a, 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 G1TDB3
Every structure of UniProt G1TLT8
Every structure of UniProt G1TFE8
Every structure of UniProt G1SS70
Every structure of UniProt G1TIB4
Every structure of UniProt G1TNM3
Every structure of UniProt G1T8A2
Every structure of UniProt G1TFM5
Every structure of UniProt G1SK22
Every structure of UniProt G1TM55
Every structure of UniProt G1SJB4
Every structure of UniProt G1SVB0
Every structure of UniProt G1TJW1
Every structure of UniProt B7NZS8
Every structure of UniProt G1TPV3
Every structure of UniProt G1SFR8
Every structure of UniProt G1U0Q2
Every structure of UniProt G1SGX4
Every structure of UniProt G1TU13
Every structure of UniProt G1TPG3
Every structure of UniProt G1TN62
Every structure of UniProt G1SIZ2
Every structure of UniProt G1TM82
Every structure of UniProt A0A5F9CBF4
Every structure of UniProt P0DTD1
Every structure of UniProt G1TK17
Every structure of UniProt G1TRM4
Every structure of UniProt G1SP51
Every structure of UniProt G1U472
Every structure of UniProt G1TG89
Every structure of UniProt G1SZ47
Every structure of UniProt G1TZ76
Elsewhere: RCSB PDB 7JQB · PDBe 7JQB · UniProt G1TDB3 · UniProt G1TLT8 · UniProt G1TFE8 · UniProt G1SS70 · UniProt G1TIB4 · UniProt G1TNM3 · UniProt G1T8A2 · UniProt G1TFM5 · UniProt G1SK22 · UniProt G1TM55 · UniProt G1SJB4 · UniProt G1SVB0 · UniProt G1TJW1 · UniProt B7NZS8 · UniProt G1TPV3 · UniProt G1SFR8 · UniProt G1U0Q2 · UniProt G1SGX4 · UniProt G1TU13 · UniProt G1TPG3 · UniProt G1TN62 · UniProt G1SIZ2 · UniProt G1TM82 · UniProt A0A5F9CBF4 · UniProt P0DTD1 · UniProt G1TK17 · UniProt G1TRM4 · UniProt G1SP51 · UniProt G1U472 · UniProt G1TG89 · UniProt G1SZ47 · UniProt G1TZ76

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