SARS-CoV-2 Protein Homology Models

Models of the SARS-CoV-2 proteins – downloadable in PDB format on this page – were constructed using the AS2TS software package

Protein sequences come from the SARS-CoV-2 reference genome here and here.  Names and annotations in the following table come from that source.

The last part of each PDB file name indicates the model template by PDB ID and chain.  For example, the nsp1 model is based on template PDB 2gdt, chain A.  Each file includes additional information in REMARK fields.

Name

Long name

Annotation

Protein

Length

Coverage

Homology models

nsp1

leader protein

 

YP_009725297.1

18013-127

00_xxsBL62.Q76802_24_1.nCoV_nsp1_QHU36823_n.2gdt_A.pdb

nsp2

   

YP_009725298.1

638  

nsp3

 

conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP);

YP_009725299.1

19451-111 207-373 413-676 746-1064 1089-1203

00_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.6w9c_A.pdb

03_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.5e6j_A.pdb

06_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.5tl7_B.pdb

12_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.2w2g_A.pdb

16_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.6w02_B.pdb

22_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.2k87_A.pdb

24_xxsBL62.Q76802_24_3.nCoV_nsp3_QHU36823_n.2gri_A.pdb

nsp4

nsp4B_TM

contains transmembrane domain 2 (TM2);

YP_009725300.1

500403-499

01_xxsBL62.Q76802_24_5.nCoV_nsp4_QHU36823_n.3vcb_A.pdb

02_xxsBL62.Q76802_24_5.nCoV_nsp4_QHU36823_n.3gzf_A.pdb

nsp5

3C-like proteinase

nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003);

YP_009725301.1

3061-306

76_xxsBL62.Q76802_24_6.nCoV_nsp5_QHU36823_n.5r82_A.pdb

77_xxsBL62.Q76802_24_6.nCoV_nsp5_QHU36823_n.6lu7_A.pdb

82_xxsBL62.Q76802_24_6.nCoV_nsp5_QHU36823_n.3tnt_A.pdb

nsp6

nsp6_TM

putative transmembrane domain

YP_009725302.1

290  

nsp7

   

YP_009725303.1

831-83

00_xxsBL62.Q76802_24_8.nCoV_nsp7_QHU36823_n.6m71_C.pdb

03_xxsBL62.Q76802_24_8.nCoV_nsp7_QHU36823_n.5f22_A.pdb

04_xxsBL62.Q76802_24_8.nCoV_nsp7_QHU36823_n.3ub0_B.pdb

nsp8

   

YP_009725304.1

1981-191

04_xxsBL62.Q76802_24_8.nCoV_nsp7_QHU36823_n.3ub0_B.pdb

nsp9

 

ssRNA-binding protein;

YP_009725305.1

1131-113

00_xxsBL62.Q76822_25_10.nCoV_nsp9_QHU36823_n.6w9q_A.pdb

01_xxsBL62.Q76802_24_10.nCoV_nsp9_QHU36823_n.6w4b_B.pdb

05_xxsBL62.Q76802_24_10.nCoV_nsp9_QHU36823_n.1uw7_A.pdb

nsp10

nsp10_CysHis

formerly known as growth-factor-like protein (GFL);

YP_009725306.1

1391-131

05_xxsBL62.Q76802_24_11.nCoV_nsp10_QHU36823_s.5c8t_A.pdb

07_xxsBL62.Q76802_24_11.nCoV_nsp10_QHU36823_s.5nfy_N.pdb

         

nsp12

RNA-dependent RNA polymerase

NiRAN and RdRp

YP_009725307.1

9321-932

00_xxsBL62.Q76802_24_12.nCoV_nsp12_QHU36823_.6m71_A.pdb

00_xxsBL62.Q76822_25_12.nCoV_nsp12_QHU36823_.7btf_A.pdb

01_xxsBL62.Q76802_24_12.nCoV_nsp12_QHU36823_.6nur_A.pdb

nsp13

helicase

nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase

YP_009725308.1

6011-596

00_xxsBL62.Q76802_24_13.nCoV_nsp13_QHU36823_.6jyt_A.pdb

01_xxsBL62.Q76802_24_13.nCoV_nsp13_QHU36823_.5wwp_B.pdb

nsp14

3'-to-5' exonuclease"

nsp14A2_ExoN and nsp14B_NMT;

YP_009725309.1

5271-525

00_xxsBL62.Q76802_24_14.nCoV_nsp14_QHU36823_.5c8s_B.pdb

01_xxsBL62.Q76802_24_14.nCoV_nsp14_QHU36823_.5c8t_B.pdb

nsp15

endoRNAse

nsp15-A1 and nsp15B-NendoU;

YP_009725310.1

3461-345

00_xxsBL62.Q76802_24_15.nCoV_nsp15_QHU36823_.6w01_A.pdb

05_xxsBL62.Q76802_24_15.nCoV_nsp15_QHU36823_.2h85_A.pdb

nsp16

2'-O-ribose methyltransferase

nsp16_OMT; 2'-o-MT;

YP_009725311.1

2981-298

03_xxsBL62.Q76802_24_16.nCoV_nsp16_QHU36823_.6w4h_A.pdb

04_xxsBL62.Q76802_24_16.nCoV_nsp16_QHU36823_.6w61_A.pdb

S

spike

surface glycoprotein

YP_009724390.1

127318-1147

00_xxsBL62.Q76802_24_17.nCoV_Spike_QHU36824_.6vsb_C.pdb

06_xxsBL62.Q76802_24_17.nCoV_Spike_QHU36824_.6vxx_B.pdb

12_xxsBL62.Q76802_24_17.nCoV_Spike_QHU36824_.6acc_A.pdb

23_xxsBL62.Q76802_24_17.nCoV_Spike_QHU36824_.6m0j_E.pdb

24_xxsBL62.Q76802_24_17.nCoV_Spike_QHU36824_.6lzg_B.pdb

25_xxsBL62.Q76802_24_17.nCoV_Spike_QHU36824_.6w41_C.pdb

ORF3a

ORF3a protein

 

YP_009724391.1

275  

E

envelope protein

ORF4; structural protein; E protein

YP_009724392.1

75

00_xxsBL62.Q76802_24_19.nCoV_E_QHU36826_E.5x29_A.pdb

01_xxsBL62.Q76802_24_19.nCoV_E_QHU36826_E.2mm4_A.pdb

M

membrane glycoprotein

ORF5; structural protein

YP_009724393.1

222  

ORF6

ORF6 protein

 

YP_009724394.1

61  

ORF7a

ORF7a protein

 

YP_009724395.1

12115-98

00_xxsBL62.Q76802_24_22.nCoV_ORF7a_QHU36829_.1xak_A.pdb

01_xxsBL62.Q76802_24_22.nCoV_ORF7a_QHU36829_.1yo4_A.pdb

ORF7b

   

YP_009725318.1

43  

ORF8

ORF8 protein

 

YP_009724396.1

121  

N

nucleocapsid phosphoprotein

ORF9; structural protein

YP_009724397.2

41947-173 250-364

00_xxsBL62.Q76822_25_24.nCoV_N_QHU36831_N.6yi3_A.pdb

07_xxsBL62.Q76802_24_24.nCoV_N_QHU36831_N.6m3m_B.pdb

09_xxsBL62.Q76802_24_24.nCoV_N_QHU36831_N.6vyo_D.pdb

15_xxsBL62.Q76802_24_24.nCoV_N_QHU36831_N.2cjr_A.pdb

ORF10

ORF10 protein

 

YP_009725255.1

38  


Models/methods: Molecular docking | Single-point GBSA | “Fusion” machine learning model | MD-trajectory-average GBSA | Safety and pharmacokinetic property predictions