SARS-CoV-2 3D

Host translation inhibitor nsp1

UniProt ITasser SWISS Models alphafold D3Targets-2019-nCoV

Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response

Models/PDB

No model built for protein with good structural coverage represented in PDB

Models/PDB	Model Chains_ID	Selected Templates	Model-Quality (MolProbity)	PDB Coverage	Model Coverage	Sequence Length	Oligomer States	Oligomer Interfaces	Model information
nsp1 Download Pdb file	i	2GDT_A; 5C5S_A; 6ZLW_i;	1.54	17.77%	100.00%	180	Hetero 35-mer	nsp1 Download interfaces pdf	nsp1 Download model information txt

Models/PDB

Model Chains_ID

Selected Templates

Model-Quality (MolProbity)

PDB Coverage

Model Coverage

Sequence Length

Oligomer States

Oligomer Interfaces

Model information

nsp1

Download Pdb file

2GDT_A; 5C5S_A; 6ZLW_i;

1.54

17.77%

100.00%

180

Hetero 35-mer

nsp1

Download interfaces pdf

nsp1

Download model information txt

Binding Site Predictions

The fpocket calculation in this table only for structure present in the Model/PDB table above.

fpocket	pocket score	drug score	hydrophobicity score	polarity score
pocket0_nsp1	32.65	0.24	35.92	6
pocket1_nsp1	27.13	0.01	21.94	5
pocket2_nsp1	26.17	0.06	25.5	8
pocket3_nsp1	25.02	0.02	23.33	5
pocket4_nsp1	22.89	0.02	18.9	6
pocket5_nsp1	22.21	0.01	-16.13	6
pocket6_nsp1	21.42	0.01	5.83	6
pocket7_nsp1	19.85	0.01	13.33	6

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Other PDB Hits

ID	Method	Resolution Å	Chains	Links
6zme	CRYO_EM	3		PDBe RCSB PDB
6zok	CRYO_EM	2.8		PDBe RCSB PDB
6zlw	CRYO_EM	2.7		PDBe RCSB PDB
6zm7	CRYO_EM	2.7		PDBe RCSB PDB
6zn5	CRYO_EM	3.2		PDBe RCSB PDB
6zon	CRYO_EM	3		PDBe RCSB PDB
6zp4	CRYO_EM	2.9		PDBe RCSB PDB
6zoj	CRYO_EM	2.8		PDBe RCSB PDB
6zmi	CRYO_EM	2.6		PDBe RCSB PDB
6zmo	CRYO_EM	3.1		PDBe RCSB PDB
6zmt	CRYO_EM	3		PDBe RCSB PDB
7k3n	X-RAY	1.65	A;	PDBe RCSB PDB
7k5i	CRYO_EM	2.9	1;	PDBe RCSB PDB
7k7p	X-RAY	1.77	B;	PDBe RCSB PDB

SAR CoV-2 & Human Proteins interaction

To download all protein-protein docking models please see the Help page

PPI docking	CHARMM_ENERGY	pdb_human	human_genes
4rr2D-nsp1.003.09.min Download Pdb file	-18728.02	4rr2_D	PRIM2
4rr2D-nsp1.003.18.min Download Pdb file	-18643.64	4rr2_D	PRIM2
4rr2D-nsp1.001.15.min Download Pdb file	-18637.32	4rr2_D	PRIM2
4rr2D-nsp1.003.05.min Download Pdb file	-18624.19	4rr2_D	PRIM2
4mhqA-nsp1.001.10.min Download Pdb file	-18649.63	4mhq_A	PRIM1
4mhqA-nsp1.003.16.min Download Pdb file	-18564.29	4mhq_A	PRIM1
4mhqA-nsp1.003.24.min Download Pdb file	-18562.23	4mhq_A	PRIM1
4mhqA-nsp1.001.21.min Download Pdb file	-18547.36	4mhq_A	PRIM1

Protein-Protein Interactions

We have mapped SARS CoV-2 human Protein-Protein Interactions from A SARS-CoV-2 protein interaction map reveals targets for drug repurposing human drug target interacted with SARS CoV-2 are highlighted in black arrow.