Research workbench

SARS-cov-2 NSP1 bound to a pre-40S-like ribosome complex

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

PDB: 6ZMT
Type: protein + RNA
Length: 6,923 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal protein S2; 40S…
EC: 4.2.99.18, 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, P23396, P62753, P62081, P62241, P46781, P46782, P62280, P46783, P62277, P25398, P62263, P62841, P62249, P08708, P62269, P39019, P60866, P62244, P62266, P62847, P63220, P62851, P42677, P62857, P62861, P62273, P62979, P63244, P0DTD1, Q2NL82
Ligands: ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 35 distinct chains · 28% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	40S ribosomal protein sa	protein	206	36% helix, 15% strand	P08865
C	40S ribosomal protein S3A	protein	213	24% helix, 27% strand	P61247
D	40S ribosomal protein S2	protein	218	28% helix, 27% strand	P15880
E	40S ribosomal protein S4, X isoform	protein	262	12% helix, 31% strand	P62701
F	40S ribosomal protein S3 (EC 4.2.99.18)	protein	225	31% helix, 26% strand	P23396
G	40S ribosomal protein S6	protein	230	27% helix, 24% strand	P62753
H	40S ribosomal protein S7	protein	186	37% helix, 23% strand	P62081
I	40S ribosomal protein S8	protein	205	28% helix, 26% strand	P62241
J	40S ribosomal protein S9	protein	180	44% helix, 4% strand	P46781
K	40S ribosomal protein S5	protein	189	44% helix, 6% strand	P46782
L	40S ribosomal protein S11	protein	151	6% helix, 30% strand	P62280
M	40S ribosomal protein S10	protein	95	33% helix, 13% strand	P46783
N	40S ribosomal protein S13	protein	149	52% helix, 0% strand	P62277
O	40S ribosomal protein S12	protein	123	33% helix, 11% strand	P25398
P	40S ribosomal protein S14	protein	122	24% helix, 21% strand	P62263
Q	40S ribosomal protein S15	protein	120	30% helix, 13% strand	P62841
R	40S ribosomal protein S16	protein	139	36% helix, 20% strand	P62249
S	40S ribosomal protein S17	protein	130	46% helix, 6% strand	P08708
T	40S ribosomal protein S18	protein	143	39% helix, 7% strand	P62269
U	40S ribosomal protein S19	protein	144	49% helix, 10% strand	P39019
V	40S ribosomal protein S20	protein	101	24% helix, 38% strand	P60866
W	40S ribosomal protein S15A	protein	129	33% helix, 28% strand	P62244
X	40S ribosomal protein S23	protein	141	23% helix, 29% strand	P62266
Y	40S ribosomal protein S24	protein	124	32% helix, 27% strand	P62847
Z	40S ribosomal protein S21	protein	82	21% helix, 27% strand	P63220
a	40S ribosomal protein S25	protein	72	44% helix, 17% strand	P62851
b	40S ribosomal protein S27	protein	82	0% helix, 28% strand	P42677
d	40S ribosomal protein S28	protein	61	0% helix, 41% strand	P62857
e	40S ribosomal protein S30	protein	56	30% helix, 0% strand	P62861
f	40S ribosomal protein S29	protein	54	20% helix, 9% strand	P62273
g	Ubiquitin-40S ribosomal protein S27A	protein	64	11% helix, 19% strand	P62979
j	Receptor of activated protein C kinase 1	protein	314	1% helix, 45% strand	P63244
2	18S ribosomal RNA	rna	1569	—	—
i	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	29	69% helix, 0% strand	P0DTD1
u	Pre-rRNA-processing protein TSR1 homolog	protein	615	20% helix, 28% strand	Q2NL82

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains f, g

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	1006	0.89	0.92	126	empty
2	1089	0.88	0.91	94	empty
3	1015	0.88	0.90	101	empty
4	916	0.87	0.89	98	empty
5	1028	0.86	0.88	93	empty

Interfaces

94 interfaces between chains.

G–2 · 5346 Å² buried · 114 hydrogen bonds · protein-nucleic
I–2 · 4322 Å² buried · 107 hydrogen bonds · protein-nucleic
E–2 · 3779 Å² buried · 72 hydrogen bonds · protein-nucleic
J–2 · 3630 Å² buried · 77 hydrogen bonds · protein-nucleic
X–2 · 3330 Å² buried · 55 hydrogen bonds · protein-nucleic

Compared structures

6ZMT · SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex · the same entry in another collection · chain L against L, 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 P23396
Every structure of UniProt P62753
Every structure of UniProt P62081
Every structure of UniProt P62241
Every structure of UniProt P46781
Every structure of UniProt P46782
Every structure of UniProt P62280
Every structure of UniProt P46783
Every structure of UniProt P62277
Every structure of UniProt P25398
Every structure of UniProt P62263
Every structure of UniProt P62841
Every structure of UniProt P62249
Every structure of UniProt P08708
Every structure of UniProt P62269
Every structure of UniProt P39019
Every structure of UniProt P60866
Every structure of UniProt P62244
Every structure of UniProt P62266
Every structure of UniProt P62847
Every structure of UniProt P63220
Every structure of UniProt P62851
Every structure of UniProt P42677
Every structure of UniProt P62857
Every structure of UniProt P62861
Every structure of UniProt P62273
Every structure of UniProt P62979
Every structure of UniProt P63244
Every structure of UniProt P0DTD1
Every structure of UniProt Q2NL82
Elsewhere: RCSB PDB 6ZMT · PDBe 6ZMT · UniProt P08865 · UniProt P61247 · UniProt P15880 · UniProt P62701 · UniProt P23396 · UniProt P62753 · UniProt P62081 · UniProt P62241 · UniProt P46781 · UniProt P46782 · UniProt P62280 · UniProt P46783 · UniProt P62277 · UniProt P25398 · UniProt P62263 · UniProt P62841 · UniProt P62249 · UniProt P08708 · UniProt P62269 · UniProt P39019 · UniProt P60866 · UniProt P62244 · UniProt P62266 · UniProt P62847 · UniProt P63220 · UniProt P62851 · UniProt P42677 · UniProt P62857 · UniProt P62861 · UniProt P62273 · UniProt P62979 · UniProt P63244 · UniProt P0DTD1 · UniProt Q2NL82

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