Research workbench

SARS-cov-2-NSP1-40S complex, focused on body

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

PDB: 6ZOK
Type: protein + RNA
Length: 4,202 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S ribosomal RNA; 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal…
EC: 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
UniProt: P08865, P61247, P15880, P62701, P62753, P62081, P62241, P46781, P62280, P62277, P62263, P08708, P63220, P62244, P62266, P62847, P62854, P42677, P62861, P0DTD1, P62945
Ligands: MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 22 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S ribosomal RNA	rna	1232	—	—
A	40S ribosomal protein sa	protein	216	39% helix, 14% strand	P08865
B	40S ribosomal protein S3A	protein	213	29% helix, 35% strand	P61247
C	40S ribosomal protein S2	protein	218	33% helix, 27% strand	P15880
E	40S ribosomal protein S4, X isoform	protein	262	18% helix, 33% strand	P62701
G	40S ribosomal protein S6	protein	230	28% helix, 24% strand	P62753
H	40S ribosomal protein S7	protein	186	41% helix, 23% strand	P62081
I	40S ribosomal protein S8	protein	205	31% helix, 25% strand	P62241
J	40S ribosomal protein S9	protein	180	51% helix, 6% strand	P46781
L	40S ribosomal protein S11	protein	151	7% helix, 32% strand	P62280
N	40S ribosomal protein S13	protein	149	58% helix, 0% strand	P62277
O	40S ribosomal protein S14	protein	135	25% helix, 25% strand	P62263
R	40S ribosomal protein S17	protein	51	18% helix, 12% strand	P08708
V	40S ribosomal protein S21	protein	83	20% helix, 27% strand	P63220
W	40S ribosomal protein S15A	protein	129	32% helix, 27% strand	P62244
X	40S ribosomal protein S23	protein	141	26% helix, 29% strand	P62266
Y	40S ribosomal protein S24	protein	124	35% helix, 29% strand	P62847
a	40S ribosomal protein S26	protein	101	16% helix, 23% strand	P62854
b	40S ribosomal protein S27	protein	82	7% helix, 27% strand	P42677
e	40S ribosomal protein S30	protein	56	23% helix, 0% strand	P62861
j	Non-structural protein 1 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-)	protein	33	64% helix, 0% strand	P0DTD1
h	60S ribosomal protein L41	protein	25	72% helix, 0% strand	P62945

Ligands and binding sites

MG · Magnesium ion · metal · 109 copies · chains 2, a, h, j, N, E, X, I, G, O, L
ZN · Zinc ion · metal · chains a

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	0.88	0.90	126	MG
2	924	0.87	0.90	72	empty
3	914	0.86	0.88	107	MG
4	1051	0.85	0.87	82	MG
5	1089	0.85	0.87	83	MG

Interfaces

56 interfaces between chains.

2–G · 5130 Å² buried · 116 hydrogen bonds · protein-nucleic
2–I · 4240 Å² buried · 92 hydrogen bonds · protein-nucleic
2–E · 3724 Å² buried · 65 hydrogen bonds · protein-nucleic
2–J · 3568 Å² buried · 66 hydrogen bonds · protein-nucleic
2–X · 3307 Å² buried · 73 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6ZOK · SARS-CoV-2-Nsp1-40S complex, focused on body · the same entry in another collection · chain I against I, 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 P08865
Every structure of UniProt P61247
Every structure of UniProt P15880
Every structure of UniProt P62701
Every structure of UniProt P62753
Every structure of UniProt P62081
Every structure of UniProt P62241
Every structure of UniProt P46781
Every structure of UniProt P62280
Every structure of UniProt P62277
Every structure of UniProt P62263
Every structure of UniProt P08708
Every structure of UniProt P63220
Every structure of UniProt P62244
Every structure of UniProt P62266
Every structure of UniProt P62847
Every structure of UniProt P62854
Every structure of UniProt P42677
Every structure of UniProt P62861
Every structure of UniProt P0DTD1
Every structure of UniProt P62945
Elsewhere: RCSB PDB 6ZOK · PDBe 6ZOK · UniProt P08865 · UniProt P61247 · UniProt P15880 · UniProt P62701 · UniProt P62753 · UniProt P62081 · UniProt P62241 · UniProt P46781 · UniProt P62280 · UniProt P62277 · UniProt P62263 · UniProt P08708 · UniProt P63220 · UniProt P62244 · UniProt P62266 · UniProt P62847 · UniProt P62854 · UniProt P42677 · UniProt P62861 · UniProt P0DTD1 · UniProt P62945

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