SARS-CoV-2 3D

Helicase nsp13

UniProt ITasser SWISS Models alphafold D3Targets-2019-nCoV

Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium

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
nsp13 Download Pdb file	E,F	6M5I; 6YYT; 7C2K; 6XEZ;	2.78	100.00%	100%	601	Hetero 6-mer	nsp13 Download interfaces pdf	nsp13 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

nsp13

Download Pdb file

E,F

6M5I; 6YYT; 7C2K; 6XEZ;

2.78

100.00%

100%

601

Hetero 6-mer

nsp13

Download interfaces pdf

nsp13

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_nsp13	31.53	0.04	-1	11
pocket1_nsp13	29.69	0.05	20.92	5
pocket2_nsp13	29.66	0.02	14.91	8

UniProt Viewer

Other PDB Hits

ID	Method	Resolution Å	Chains	Links
7cxm	CRYO_EM	2.9	E, F;	PDBe RCSB PDB
7cxn	CRYO_EM	3.84	E, F;	PDBe RCSB PDB
6zsl	X-RAY	1.94	A	PDBe RCSB PDB
6xez	CRYO_EM	3.5	A,B,C,D,E,F	PDBe RCSB PDB
5rmb	X-RAY	2.21	A, B;	PDBe RCSB PDB
5rm5	X-RAY	2.06	A, B;	PDBe RCSB PDB
5rlp	X-RAY	2.56	A, B;	PDBe RCSB PDB
5rmc	X-RAY	2.15	A, B;	PDBe RCSB PDB
5rlg	X-RAY	1.96	B, A;	PDBe RCSB PDB
5rlf	X-RAY	2.24	A, B;	PDBe RCSB PDB
5rlq	X-RAY	2.23	A, B;	PDBe RCSB PDB
5rm4	X-RAY	2.96	B, A;	PDBe RCSB PDB
5rls	X-RAY	2.28	A, B;	PDBe RCSB PDB
5rm6	X-RAY	2.13	A, B;	PDBe RCSB PDB
5rld	X-RAY	2.23	A, B;	PDBe RCSB PDB
5rma	X-RAY	1.89	A, B;	PDBe RCSB PDB
5rle	X-RAY	2.27	A, B;	PDBe RCSB PDB
5rm7	X-RAY	1.84	A, B;	PDBe RCSB PDB
5rlr	X-RAY	2.32	A, B;	PDBe RCSB PDB
5rme	X-RAY	2.23	B, A;	PDBe RCSB PDB
5rlv	X-RAY	2.21	A, B;	PDBe RCSB PDB
5rl7	X-RAY	1.89	B, A;	PDBe RCSB PDB
5rm3	X-RAY	2.09	B, A;	PDBe RCSB PDB
5rm2	X-RAY	1.82	A, B;	PDBe RCSB PDB
5rl6	X-RAY	1.92	A, B;	PDBe RCSB PDB
5rlw	X-RAY	1.97	A, B;	PDBe RCSB PDB
5rmd	X-RAY	1.92	A, B;	PDBe RCSB PDB
5rmf	X-RAY	2.23	A, B;	PDBe RCSB PDB
5rlb	X-RAY	1.98	A, B;	PDBe RCSB PDB
5rm0	X-RAY	1.91	A, B;	PDBe RCSB PDB
5rlu	X-RAY	2.35	A, B;	PDBe RCSB PDB
5rlt	X-RAY	2.43	A, B;	PDBe RCSB PDB
5rm1	X-RAY	1.9	A, B;	PDBe RCSB PDB
5rlc	X-RAY	1.92	A, B;	PDBe RCSB PDB
5rmg	X-RAY	2.12	A, B;	PDBe RCSB PDB
5rln	X-RAY	2.15	A, B;	PDBe RCSB PDB
5rmj	X-RAY	2.1	B, A;	PDBe RCSB PDB
5rly	X-RAY	2.43	A, B;	PDBe RCSB PDB
5rl8	X-RAY	2.21	B, A;	PDBe RCSB PDB
5rl9	X-RAY	1.79	A, B;	PDBe RCSB PDB
5rmk	X-RAY	2.08	A, B;	PDBe RCSB PDB
5rlo	X-RAY	2.1	A, B;	PDBe RCSB PDB
5rmi	X-RAY	2.12	A, B;	PDBe RCSB PDB
5rlm	X-RAY	1.86	A, B;	PDBe RCSB PDB
5rlz	X-RAY	1.97	B, A;	PDBe RCSB PDB
5rll	X-RAY	2.08	A, B;	PDBe RCSB PDB
5rmh	X-RAY	2.02	A, B;	PDBe RCSB PDB
5rml	X-RAY	2.43	B, A;	PDBe RCSB PDB
5rlh	X-RAY	2.38	A, B;	PDBe RCSB PDB
5rli	X-RAY	2.26	A, B;	PDBe RCSB PDB
5rmm	X-RAY	2.2	A, B;	PDBe RCSB PDB
5rm9	X-RAY	2.08	A, B;	PDBe RCSB PDB
5rlk	X-RAY	1.96	A, B;	PDBe RCSB PDB
5rlj	X-RAY	1.88	A, B;	PDBe RCSB PDB
5rm8	X-RAY	2.14	A, B;	PDBe RCSB PDB

Predictions of Mutations

pdb_id	mutations	deepddg	maestro	mCSM_ppi	mCSM_Stability	imutant	provean
6xez	G206N	-0.731	-0.763284	-0.29	-0.379	Decrease	-0.564
6xez	T61W	-0.659	-0.699801	-0.23	-0.766	Decrease	-5.99
6xez	T61Y	-0.962	-0.692309	-0.092	-0.496	Increase	-5.851
6xez	T61F	-0.446	-0.686376	-0.275	-0.751	Decrease	-5.99
6xez	G206Q	-0.238	-0.653343	-0.196	-0.655	Decrease	-2.028
6xez	G206E	-0.664	-0.64604	-0.397	-0.845	Decrease	-1.88
6xez	G206M	-0.657	-0.645964	-0.041	-0.379	Decrease	-3.155
6xez	G206S	-0.327	-0.636457	-0.005	-0.491	Decrease	0.178
6xez	G206L	-0.681	-0.617086	-0.411	-0.333	Decrease	-3.979
6xez	G206P	-1.223	-0.616515	-0.405	-0.28	Decrease	-2.922
6xez	G206F	-0.664	-0.613705	0.23	-0.964	Decrease	-4.121
6xez	G206C	-0.638	-0.609875	0.119	-0.606	Decrease	-3.521
6xez	G206D	-0.223	-0.608584	-0.316	-0.698	Decrease	-1.414
6xez	G206T	-0.546	-0.60704	-0.058	-0.574	Decrease	-0.801
6xez	G206W	-0.409	-0.583119	0.215	-1.176	Decrease	-4.242
6xez	T61Q	-1.203	-0.581819	-0.638	-0.523	Decrease	-4.558
6xez	G206I	-0.61	-0.579976	-0.411	-0.333	Decrease	-4.079
6xez	T61E	-0.52	-0.57809	-0.689	0.002	Decrease	-4.291
6xez	T61D	-1.412	-0.576673	-0.63	0.051	Decrease	-4.634
6xez	G206Y	-0.616	-0.565331	0.269	-0.809	Decrease	-3.855
6xez	K323Q	-0.048	-0.564906	-1.009	-0.338	Decrease	-3.133
6xez	K323E	-0.045	-0.561148	-0.866	-0.105	Decrease	-3.133
6xez	T61M	-0.541	-0.515165	0.149	0.06	Decrease	-4.968
6xez	D583E	-0.014	-0.506961	-0.322	-0.593	Increase	-1.642
6xez	G206H	-0.668	-0.497931	0.494	-0.624	Decrease	-2.79
6xez	T61H	-1.803	-0.492672	0.153	-0.844	Decrease	-5.646
6xez	K192I	-0.667	-0.486021	-0.44	0.199	Decrease	-7.857
6xez	G206R	-0.203	-0.485633	-0.549	-0.419	Decrease	-2.491
6xez	G206K	-0.117	-0.484775	-0.298	-0.861	Decrease	-1.915
6xez	G206V	-0.84	-0.483482	-0.405	-0.28	Decrease	-3.641
6xez	T61N	-1.573	-0.47984	-0.783	-0.347	Decrease	-3.985
6xez	G206A	-0.784	-0.470299	-0.407	-0.277	Decrease	-1.729
6xez	K323D	-0.164	-0.463564	-0.825	-0.184	Decrease	-4.696
6xez	N268W	0.321	-0.455008	-1.516	-0.375	Decrease	-2.2
6xez	N562M	0.359	-0.446836	-0.97	0.314	Increase	-7.733
6xez	N562L	1.015	-0.446491	-1.072	0.083	Increase	-8.7
6xez	T61I	-0.525	-0.442641	-0.399	-0.05	Decrease	-5.145
6xez	A316Y	0.287	-0.43583	-0.752	-1.19	Decrease	-4.967
6xez	T61L	-0.729	-0.435065	-0.399	-0.05	Decrease	-5.107
6xez	A316W	0.607	-0.430195	-0.969	-1.529	Decrease	-5.95
6xez	K323P	-0.447	-0.42694	-1.149	0.172	Increase	-4.71
6xez	A4W	0.183	-0.425353	0.319	-1.537	Decrease	-3.032
6xez	T61P	-1.443	-0.422974	-0.395	-0.14	Decrease	-4.928
6xez	A316L	0.947	-0.41416	-1.065	-0.658	Decrease	-4.294
6xez	K192L	-0.604	-0.413556	-0.44	0.199	Increase	-6.873
6xez	K323S	-0.179	-0.413488	-0.838	-0.776	Decrease	-3.527
6xez	N268C	-0.461	-0.410211	-1.412	-0.04	Decrease	-3.267
6xez	N519W	0.157	-0.409611	-0.898	-0.542	Decrease	-9.896
6xez	N562W	-0.252	-0.408028	-1.48	-0.594	Decrease	-9.667
6xez	P175W	-0.568	-0.40738	-1.221	-1.029	Decrease	-10.817

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
3ovvA-nsp13.003.08.min Download Pdb file	-29061.2	3ovv_A	PRKACA
3ovvA-nsp13.003.18.min Download Pdb file	-29044.49	3ovv_A	PRKACA
3ovvA-nsp13.003.17.min Download Pdb file	-29008.45	3ovv_A	PRKACA
3ovvA-nsp13.003.00.min Download Pdb file	-29007.59	3ovv_A	PRKACA
6nt9A-nsp13.001.00.min Download Pdb file	-37334.6	6nt9_A	TBK1
6nt9A-nsp13.003.04.min Download Pdb file	-37274.6	6nt9_A	TBK1
6nt9A-nsp13.003.26.min Download Pdb file	-37248.07	6nt9_A	TBK1
6nt9A-nsp13.003.10.min Download Pdb file	-37239.98	6nt9_A	TBK1

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.